Freesurfer

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Armin Allahverdy

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Apr 9, 2024, 2:53:50 PM4/9/24
to HCP-Users
Hi
I'm runing the "FreeSurferPipeline-v5.3.0-HCP.sh" on my own data, but I encounter the following error:
 mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated

setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
thresholding curvature at 99.90% level
error: No such file or directory
error: MRISread(lh.inflated): could not open file
error: No such file or directory
error: mris_curvature: could not read surface file lh.inflated

I checked the folder and figured out these two file (lh.inflated, and rh.inflated) are not exist, and I only have (lh.inflated.nofix, and rh.inflated.nofix)

How can I solve this issue?

Tim Coalson

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Apr 9, 2024, 7:28:21 PM4/9/24
to hcp-...@humanconnectome.org
What version of freesurfer are you using it with?

Tim


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Glasser, Matt

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Apr 9, 2024, 7:34:57 PM4/9/24
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Also, that is legacy code and is not currently tested frequently.


Matt.

 

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Armin Allahverdy

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Apr 9, 2024, 7:37:02 PM4/9/24
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I’m using freesurfer 7

Armin Allahverdy

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Apr 9, 2024, 7:37:58 PM4/9/24
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Which code is the updated one?
How can I have it?

Glasser, Matt

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Apr 9, 2024, 7:40:08 PM4/9/24
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We recommend FreeSurfer 6 with the mainline pipeline.  FreeSurfer 7 has some quality regressions and FreeSurfer 5.3 is really old at this point.


Matt.

Armin Allahverdy

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Apr 9, 2024, 7:47:23 PM4/9/24
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Which hcp are you referring to?
How can I find it 

Glasser, Matt

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Apr 9, 2024, 7:48:51 PM4/9/24
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Armin Allahverdy

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Apr 9, 2024, 7:49:42 PM4/9/24
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Thanks 

Armin Allahverdy

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Apr 10, 2024, 2:27:35 PM4/10/24
to HCP-Users, Armin Allahverdy

Hi Developers

I’m using FreeSurfer6, and this code:

${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh \

--subjectDIR="${SUBJECTS_dIR}" \

--subject="${SUBJECT_Id}" \

--t1="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore.nii.gz" \

--t2="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T2w_acpc_dc_restore.nii.gz" \

--t1brain="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore_brain.nii.gz"

 

But I encounter to this error:

mri_normalize -sigma 8 -erode 1 -min_dist 1 -surface ../surf/lh.white.preaparc.rawavg identity.nofile -surface ../surf/rh.white.preaparc.rawavg identity.nofile rawavg.cmdc.mgz rawavg.norm.mgz

using Gaussian smoothing of bias field, sigma=8.000

eroding interior of surface 1 times

retaining  nonmaximum suppressed points that are at least 1.000mm from the boundary

reading mri_src from rawavg.cmdc.mgz...

Copying mri_dst from mri_src

error: No such file or directory

error: MRISread(../surf/lh.white.preaparc.rawavg): could not open file

error: No such file or directory

error: mri_normalize: could not surface ../surf/lh.white.preaparc.rawavg

ERROR:

Linux EW23-03270 4.4.0-19041-Microsoft #3996-Microsoft Thu Jan 18 16:36:00 PST 2024 x86_64 x86_64 x86_64 GNU/Linux

Glasser, Matt

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Apr 10, 2024, 2:41:14 PM4/10/24
to hcp-...@humanconnectome.org, Armin Allahverdy

Perhaps you should post the full logs, off-list if needed.

Armin Allahverdy

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Apr 10, 2024, 2:44:58 PM4/10/24
to HCP-Users, glas...@wustl.edu, Armin Allahverdy
This is the log that I got.
recon-all.log

Glasser, Matt

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Apr 10, 2024, 2:48:53 PM4/10/24
to hcp-...@humanconnectome.org, Armin Allahverdy

Your log says you are using FreeSurfer 7.4.1.

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