other output metrics

[Jeanette Kenley]

Good morning,

I am trying to use DSI studio's CMI to create parametric maps using the following command:

dsi_studio --action=rec --source=*.src.gz --method=3 --param0=1.25 --output=/output_folder_location --other_output=all

But the command executes with an error:

/opt/dsi-studio/dsi_studio: No match.

Am I missing a flag?  The command I run to create the source file executes without issue dsi_studio --action=src --source=/path/to/data/data.nii.gz --bval=bvals --bvec=bvecs

I also tried via the GUI on my windows desktop and I was able to create the source and FIB files, but no parametric maps, even when I have the advanced option clicked.  (see attached)

Thanks for any and all help!

Jeanette

[Fang-Cheng Yeh]

--method=4 for gqi
--method=7 for qsdr

> --
> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/0e521889-16ea-40a3-a509-cf92c0f128b2n%40googlegroups.com.

[Jeanette Kenley]

Hah!  Well, color me red.  Thanks for the feedback.

I altered the method to 4 and still got the same error.  Am I missing something else?

% /opt/dsi-studio/dsi_studio --action=rec --source=*.src.gz --method=4 --param0=1.25 --output=/DSI_studio --other_output=all
/opt/dsi-studio/dsi_studio: No match.

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtL285A_zTdMw%2BZB80%2BYt4RWSCf%3Ds0vCePLsCxQJk_0L6A%40mail.gmail.com.

[Jeanette Kenley]

Hi.  Thank you again for your assistance.

Just wanted to follow-up to see if you had any thoughts why I still wasn't getting parametric maps, even using method = 4.

Thanks,

Jeanette 

[Fang-Cheng Yeh]

Sorry I have no idea.
"No match" is not an error message from DSI Studio.
It seems to be an error from the operation system or the calling script.
Frank

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAOVJL%3DsQY7jn0im5mrfZDFsXFac%2BZ_Ctma%2Bc7jk5mKpiUf3mfQ%40mail.gmail.com.

[Jeanette Kenley]

Thanks for the reply.

Oddly when I tried the GUI I also didn't get output, but was able to get a FIB file.

Thoughts?

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJCa9MVDCkvvEfQvvZH-KyF1X7THWffuCg4CGw7xrpVAA%40mail.gmail.com.

[Fang-Cheng Yeh]

Perhaps checking the "console" button at the GUI to see if there is a hint.

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAOVJL%3DtOfWdvCYe33BzmANf0Cx_2zcRE1sXeyCdQOwk1GbSJYg%40mail.gmail.com.

[Jeanette Kenley]

Thanks, I'll check it out!

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_Qrt%2BdLdtDmUvd6KogkqEePw8Py8DOtF8hivd30CEevBdLHA%40mail.gmail.com.

[Jeanette Kenley]

Hi Frank,

I am finally able to come back around to this and I didn't get any useful information from the console output on the Linux machine, but I was able to run the command line via a windows machine (linux interface) and got the following:

It looks like the options I am requesting aren't available, which would explain the Linux "no match" error.

Thank you for your help.

Jeanette

/drives/c/Users/jkkenley/Documents/dsi_studio_64/dsi_studio_64/dsi_studio --action=rec --source=data.nii.gz.src.gz --method=4 --param0=1.25 --output=/drives/q/neonatal/diffusion/eLABe_AP_PA_tractography_604/MOD1022_V1_a/DWI_TPUP_EC/test --other_output=all
DSI Studio Mar 24 2021, Fang-Cheng Yeh
source=data.nii.gz.src.gz
action=rec
loading source...
src loaded
method=4
param0=1.25
odf_order=8
odf_resolving=0
record_odf=0
check_btable=1
output_tensor=0
output_rdi=1
num_fiber=5
r2_weighted=0
thread_count=6
half_sphere=0
scheme_balance=1
motion_correction=0
start reconstruction...
checking b-table
012=-7%,012fx=-10%,012fy=-8%,012fz=-12%,021=-0%,021fx=-3%,021fy=-3%,021fz=-4%
102=-4%,102fx=-4%,102fy=-2%,102fz=-3%,120=-0%,120fx=-3%,120fy=BEST,120fz=-1%
210=-9%,210fx=-13%,210fy=-8%,210fz=-12%,201=-6%,201fx=-7%,201fy=-6%,201fz=-6%
b-table corrected by .120fy for data.nii.gz.src.gz
GQI reconstruction
saving data.nii.gz.src.gz.gqi.1.25.fib.gz
reconstruction finished.
Warning: --output is not used. Please check command line syntax.
Warning: --other_output is not used. Please check command line syntax.

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_Qrt%2BdLdtDmUvd6KogkqEePw8Py8DOtF8hivd30CEevBdLHA%40mail.gmail.com.

[Fang-Cheng Yeh]

Mar 24 2021 version is a bit outdated. Could you use the most recent version and see if it works?

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAOVJL%3DtyHpWL-nmAkWi5A-6asqZcOPCskwuzPsyyVrZM-ygA9Q%40mail.gmail.com.

[Jeanette Kenley]

I downloaded the "dsi_studio_win_cpu" aka "CPU version if GPU doesn't work" (I don't have a GPU) and I still do not have parametric maps.  Below is my run and the listing of the folders after.

/drives/c/Users/jkkenley/Documents/dsi_studio_win_cpu/dsi_studio --action=rec --source=data.nii.gz.src.gz --method=4 --param0=1.25 --output=/drives/q/neonatal/diffusion/AP_PA_tractography_604/1022_V1_a/DWI_TPUP_EC/test --other_output=all
+ DSI Studio version: Chen"陳" command line
| DSI Studio version: Chen"陳"
| action=rec
| source=data.nii.gz.src.gz
| loop=data.nii.gz.src.gz
| + run rec
| | + open SRC file
| | | using index file for accelerated loading:data.nii.gz.src.gz.idx
| | | + opening data.nii.gz.src.gz
| | | |_3.595 s
| | |_4.657 s
| | + reconstruction parameters:
| | | method=4
| | | odf_resolving=0
| | | record_odf=0
| | | dti_no_high_b=1
| | | check_btable=0
| | | other_output=all
| | | r2_weighted=0
| | | thread_count=6
| | | param0=1.25
| | | param1=3000
| | | param2=0.05
| | |_0 ms
| | + specify mask
| | | mask=1
| | |_0 ms
| | + preprocessing
| | | preprocessing=0
| | | motion_correction=0
| | |_0 ms
| | + additional processing steps
| | | align_acpc=1
| | | + align acpc
| | | | align ap-pc
| | | | + opening ICBM152_adult.ISO.nii.gz
| | | | |_3 ms
| | | | + reading image data
| | | | |_34 ms
| | | | translocation:0.470001 4.7594 23.0326
| | | | rotation:0.179951 0.0582888 0.0675521
| | | | scaling:0.702428 0.707866 0.7
| | | | shear:0 0 0
| | | | R2 for ac-pc alignment:0.521202
| | | | + rotating
| | | | |_5.186 s
| | | |_15.344 s
| | |_15.344 s
| | output=/drives/q/neonatal/diffusion/AP_PA_tractography_604/1022_V1_a/DWI_TPUP_EC/test
| | + reconstructing GQI
| | |_49.831 s
| | + saving test.gqi.1.25.fib.gz
| | |_2.508 s
| |_1.20748 m
|_1.20767 m

 ls -lrt
. . .
drwxrwxr-x 1 Unknown+User Unknown+Group         0 Oct 19 11:51 test
drwxrwxr-x 1 Unknown+User Unknown+Group         0 Oct 24 14:56 Matlab_Least_Squares
-rw-rw-r-- 1 Unknown+User Unknown+Group 263795876 Oct 31 12:49 data.nii.gz.src.gz
-rw-rw-r-- 1 Unknown+User Unknown+Group   7146912 Oct 31 12:50 data.nii.gz.src.gz.idx
-rw-rw-r-- 1 Unknown+User Unknown+Group   5782532 Oct 31 12:58 data.nii.gz.src.gz.gqi.1.25.fib.gz

                                                                                                                                                                                                             ✔

ls test
                                                                                                                                                                                                             ✔

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJGBXx7SM3W7BsMwNOGH6hkji%3DGb-WYGvUep95ehTG%3DbQ%40mail.gmail.com.

[Fang-Cheng Yeh]

The CLI seems to run okay. I am not sure what the "parametric maps"
are. Could you provide more details?

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAOVJL%3DuOmLoRBGUdNxaTdB%2BkJ0vvF8VarQw2APmy75kFv_xLAg%40mail.gmail.com.

[Jeanette Kenley]

My apologies.  I call the MD, FA, RD, AD maps parametric maps.  Are they not output as separate files?  If not, then I'm sorry for the trouble I've caused.

I was hoping to do a direct comparison to the MD, FA, RD, etc maps I already have to see how they compare.

If they are not output as separate files, is there a way to parse them out via command line so I can create them in a loop?

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtKOk_PbrGDvJrQ1EdvbhiM%2BKt7QJyYiB_c4k9Pma8hqgw%40mail.gmail.com.

[Jeanette Kenley]

THank you for all your help!

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtKOk_PbrGDvJrQ1EdvbhiM%2BKt7QJyYiB_c4k9Pma8hqgw%40mail.gmail.com.

[Fang-Cheng Yeh]

Those maps are stored within the fib file.
You can export them by
dsi_studio --action=exp --source=test.gqi.1.25.fib.gz --export=dti_fa,ad,rd,md

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAOVJL%3Dv25AuhMPi4yMpaNNJnKBZuZNM425H%2BY5%3DSTR3OUwd2ug%40mail.gmail.com.

[Jeanette Kenley]

Fantastic!  Thank you!

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtKGRKoAbvz0wMTihhJQ%2BOxFkQBysnypV8Ocjh73A2Ppbg%40mail.gmail.com.