New subject: tkregister issue with reg-feat2anat {Disarmed}

13 Nov 2020


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Hi Dr. Greve,
Our IT team replaced the reg-feat2ant file on the university HPC. When I reran a test subject, it resulted in a "command not found" error. See attached screenshot. I notified IT and they stated the following:
"Since the only change made by admins was putting that new file in place, so they just put the old file back in place.
You can try running the script again to see if that 'command not found' error goes away. If not, then you need to report the error back to the author that provided the file. "
With the previous reg-feat2anat file, the bug I initially emailed about replicated.
Do you have any suggestions for what may be causing the error?
Thanks!
Erin
https://secure-web.cisco.com/1Xt5TzuhfYGMFSQ1E2hCKW008efsUaiJNMtBUxoHORy7dSd...
--
Erin Walsh, Ph.D.
Assistant Professor
University of North Carolina-Chapel Hill
Department of Psychiatry
Chapel Hill, NC 27599-3367
erin_walsh@med.unc.edu
pronouns: she/her
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Today's Topics:
1. Re: Extract he value of area and volume in the fsaverage for
      every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (???)
   2. Re: tkregister issue with reg-feat2anat {Disarmed}
      (Douglas N. Greve)
   3. Re: Extract he value of area and volume in the fsaverage for
      every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}
      (Douglas N. Greve)
   4. Re: Sulc maps (Douglas N. Greve)
   5. Re: Help with MRI labels (Douglas N. Greve)
   6. mris_pmake error - freadFloat: fread failed (Nasr, Shahin,Ph.D.)
   7. Support: Password Request for Ubuntu_710 to download
      Freesurfer on Windows 10 {Disarmed} (Park, James)
   8. Re: Support: Password Request for Ubuntu_710 to download
      Freesurfer on Windows 10 {Disarmed} {Disarmed} (fsbuild)
   9. Re: Help with MRI labels {Disarmed} (Alberto Del Cerro Leon)
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Message: 1
Date: Thu, 12 Nov 2020 18:39:44 +0800 (GMT+08:00)
From: ??? mengjun@csu.edu.cn
Subject: Re: [Freesurfer] Extract he value of area and volume in the
        fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
        {Disarmed}
To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu
Message-ID: 6071ada5.3fd7.175bc0a2c24.Coremail.mengjun@csu.edu.cn
Content-Type: text/plain; charset="utf-8"
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2?Blue color). Is this correct?
ColHeaders  Index SegId NVertices Area_mm2  StructName  Mean          StdDev      Min        Max       Range
              1   0    161058     81037.1   Seg0000   242940.3281    0.7312     0.0000     3.8885     3.8885
              2   1      2784     1182.3    Seg0001    3760.6619     0.2525     0.7136     1.8140     1.1005
Following is the code for extracting volumes
mri_segstats
--i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_volume.avgwf.dat (output file)
--accumulate
--sum lh_volume.sum (output file)
-----????-----
???:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU
????:2020-11-11 23:58:20 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
Sorry, try this
mri_segstats
--i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
On 11/5/2020 10:26 PM, ??? wrote:
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I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
-----????-----
???:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU
????:2020-11-05 22:37:07 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed}
Try
--slabel fsaverage lh /path/to/lh.areapial.label
On 11/2/2020 10:24 PM, ??? wrote:
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Thank you very much! I tried to extract the areas with the following codes:
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
I did not get a text file including the areas of all subjects. Is this code correct?
-----????-----
???:"Douglas N. Greve" dgreve@mgh.harvard.edu
????:2020-11-02 23:36:14 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed}
I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you input) all your subjects for that label.
On 10/30/2020 10:37 PM, ??? wrote:
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Dear Professors:
I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview  Then the value of the label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions:
(1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values?
(2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects
Best wishes
Mengjun Li
-----????-----
???:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU
????:2020-10-30 23:40:30 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject
Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology.
On 10/29/2020 9:51 PM, ??? wrote:
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Dear FreeSurfer Developers:
I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats
FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.
Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University
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Re: [Freesurfer] tkregister issue with reg-feat2anat {Disarmed}