Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

[fsbuild]

External Email - Use Caution

Hello Ali,
I would try using the RPM installer which should at least check some 
dependencies on X packages, system libraries, etc.,
https://secure-web.cisco.com/1QZVOusYuqG6pzgftW11woMO3J7wlOTz6CpOKDAkTB2PSKdv7HWkk1N4ZgDbrS9Ofxy-S0PLYnkCeiBbxFw3i6PW1_XXZ7IhEjoNtTlBrC8pfgQZxQ47oT-EE0H_Xci9GjTO2QyMiKh1avC8LxBuz-tFj4GUzYylvvNzU4dQp9nuq9gWQk6yDnjfVnf4GC14a2I0nJwT1F697l_HjoNb2mA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-CentOS8-7.1.1-1.x86_64.rpm
- R.

On Nov 5, 2020, at 22:39, Snedden, Ali 
ali.sned...@nationwidechildrens.org 
wrote:External Email - Use 
CautionHello,I’ve 
seen a couple mentions on the list-serv about difficulties using Freesurfer on 
CentOS 8. My issue is likely similar, but I have a few more 
details. I downloaded 
freesurfer-linux-centos8_x86_64-7.1.0.tar.gz. When I launch 
`freeview`, it pops up a white/empty X window for a moment and then quickly 
disappears.E.g.$ freeviewMESA-LOADER: failed to open 
swrast (search paths /usr/lib64/dri)libGL error: failed to load driver: 
swrastAborted (core dumped)I vaguely recall that the libGL errors 
_aren’t_ fatal. I’ve seen them with other X applications. Digging 
around the abort logs, I found the stack trace (seeendof 
email).Do you have thoughts on this? I thought it might be a 
VTK compatibility issue, but that is a guess at best.Best 
regards,Ali## The stack trace 
[ccpp-2020-11-05-09:15:34-22241]# cat 
core_backtrace{  "signal": 6,  "executable": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview",  
"only_crash_thread": true,  "stacktrace":   [ {  
"crash_thread": true,  "frames":  
 [ {  "address": 140352624871839 
   ,  "build_id": 
"f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc" 
   ,  "build_id_offset": 227743   
 ,  "function_name": "raise" 
   ,  "file_name": 
"/usr/lib64/libc-2.28.so"   
 }   , {  "address": 
140352624782581,  
"build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"   
 ,  "build_id_offset": 138485 
   ,  "function_name": 
"abort",  
"file_name": "/usr/lib64/libc-2.28.so"  
  }   , {  
"address": 140352824105729   
 ,  "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" 
   ,  "build_id_offset": 
1358593,  
"function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"   
 ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
   , {  "address": 140352824102018   
 ,  "build_id": 
"32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" 
   ,  "build_id_offset": 1354882   
 ,  "function_name": 
"vtkXOpenGLRenderWindow::WindowInitialize()" 
   ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
   , {  "address": 140352824096013   
 ,  "build_id": 
"32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" 
   ,  "build_id_offset": 1348877   
 ,  "function_name": 
"vtkXOpenGLRenderWindow::Start()"  
  ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
   , {  "address": 140352717995302   
 ,  "build_id": 
"c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" 
   ,  "build_id_offset": 1154342   
 ,  "function_name": 
"vtkRenderWindow::DoStereoRender()"  
  ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
   , {  "address": 140352717996715   
 ,  "build_id": 
"c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" 
   ,  "build_id_offset": 1155755   
 ,  "function_name": 
"vtkRenderWindow::DoFDRender()"   
 ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
   , {  "address": 140352718000997   
 ,  "build_id": 
"c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" 
   ,  "build_id_offset": 1160037   
 ,  "function_name": 
"vtkRenderWindow::DoAARender()"   
 ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
   , {  "address": 140352717997021   
 ,  "build_id": 
"c141e58a0e1cf92c2cbd3af5f59b2991aad943c6" 
   ,  "build_id_offset": 1156061   
 ,  "function_name": 
"vtkRenderWindow::Render()"   
 ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
   , {  "address": 140352824097713   
 ,  "build_id": 
"32cfd4cdfa276fffd5973c44ddb4da4f74f234e4" 
   ,  "build_id_offset": 1350577   
 ,  "function_name": 
"vtkXOpenGLRenderWindow::Render()"  
  ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
   , {  "address": 5878611
,  "build_id": 
"0de18d9e888c309c18e5e9450078f0fa6f19efa3" 
   ,  "build_id_offset": 1684307   
 ,  "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1..0/bin/freeview" 

[Freesurfer] Freesurfer 7.1.0 on CentOS 8.1

[Snedden, Ali]

External Email - Use Caution

Hello,

I’ve seen a couple mentions on the list-serv about difficulties using 
Freesurfer on CentOS 8.   My issue is likely similar, but I have a few more 
details.  I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.   When I 
launch `freeview`, it pops up a white/empty X window for a moment and then 
quickly disappears.

E.g.
$ freeview
MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)
libGL error: failed to load driver: swrast
Aborted (core dumped)

I vaguely recall that the libGL errors _aren’t_ fatal.  I’ve seen them with 
other X applications.  Digging around the abort logs, I found the stack trace 
(see end of email).

Do you have thoughts on this?  I thought it might be a VTK compatibility issue, 
but that is a guess at best.

Best regards,
Ali


## The stack trace 

[ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace
{   "signal": 6
,   "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
,   "only_crash_thread": true
,   "stacktrace":
  [ {   "crash_thread": true
,   "frames":
  [ {   "address": 140352624871839
,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
,   "build_id_offset": 227743
,   "function_name": "raise"
,   "file_name": "/usr/lib64/libc-2.28.so"
}
  , {   "address": 140352624782581
,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
,   "build_id_offset": 138485
,   "function_name": "abort"
,   "file_name": "/usr/lib64/libc-2.28.so"
}
  , {   "address": 140352824105729
,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
,   "build_id_offset": 1358593
,   "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
  , {   "address": 140352824102018
,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
,   "build_id_offset": 1354882
,   "function_name": 
"vtkXOpenGLRenderWindow::WindowInitialize()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
  , {   "address": 140352824096013
,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
,   "build_id_offset": 1348877
,   "function_name": "vtkXOpenGLRenderWindow::Start()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
  , {   "address": 140352717995302
,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
,   "build_id_offset": 1154342
,   "function_name": "vtkRenderWindow::DoStereoRender()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
  , {   "address": 140352717996715
,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
,   "build_id_offset": 1155755
,   "function_name": "vtkRenderWindow::DoFDRender()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
  , {   "address": 140352718000997
,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
,   "build_id_offset": 1160037
,   "function_name": "vtkRenderWindow::DoAARender()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
  , {   "address": 140352717997021
,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
,   "build_id_offset": 1156061
,   "function_name": "vtkRenderWindow::Render()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
}
  , {   "address": 140352824097713
,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
,   "build_id_offset": 1350577
,   "function_name": "vtkXOpenGLRenderWindow::Render()"
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
}
  , {   "address": 5878611
,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"
,   "build_id_offset": 1684307
,   "file_name": 
"/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
}
  , {  

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}

[李梦君]

External Email - Use Caution

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)






-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-05 22:37:07 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: 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, 李梦君 wrote:


External Email - Use Caution

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？ 

-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-02 23:36:14 (星期一)
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: 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, 李梦君 wrote:


External Email - Use Caution

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


-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-10-30 23:40:30 (星期五)
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: 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, 李梦君 wrote:


External Email - Use Caution

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] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

Thank you very much for your rapid response. I have another question.

I am following the FS Repeated Measures tutorial and therefore, I ran
this: mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.thickness.mgh --fsgd rmanova.fsgd.
However, in the  FS Group Analysis tutorial, it says that you must include
"--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with
recon-all with the -qcache option, which was my case. As I am doing
longitudinal analyses, do I have to skip this  option and just follow the
Repeated Measures tutorial or do I have to include the --cache option?

Thank you very much.
Best regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve ()
escribió:

> In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer
> your question, the first example you give is the right way to handle it.
>
>
> On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am trying to do a longitudinal repeated measures ANOVA 2x2, with two
> groups (experimental vs control) and two time points (pre and post
> treatment).
>
> Although I have run a paired t-test, now I would like to do a repeated
> measures anova 2x2, since I am doing the same analyses with other data in
> other softwares.
>
> I am trying to follow the tutorial *MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/11u6-IyY2-P7w7M4zmGiLCyaG6g2vViEpx4ag8H474t_vAcKQofRlrgzoecVmHS-zCmukHiQ4nYncdNoWgv3qseGeeJ5V9DyPr8qfYwFtrgu7s9OZWm-ZxMwuQ5ZFRq0n-rmVcPAZ0Hk-kzFtomVz5K6pII7oYat7YlIYPSB5e0Ig4auXkKYY9vdGnvAE3T5jbnApRosUxoICfXaCSW4-Fw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
> ,
> but I have several doubts when designing the FSGD file as well as the
> contrasts.
>
> How should it be the FSGD file?
>
> I have seen in a previous post the following design for the same number fo
> groups and time points:
>
> GroupDescriptorFile 1
>
> Class Subject1
>
> Class Subject2
>
> Variables Tp1vsTp2.GrExp
>Tp1vsTp2.GrControl
>
> Input   Subject1_time1  Subject1 1
> 0
>
> Input   Subject1_time2  Subject1-10
>
> Input   Subject2_time1  Subject2 0
> 1
>
> Input   Subject2_time2  Subject02   0
> -1
>
>
>
> Design matrix:
>
> 1 0 1 0
>
> 1 0 -1 0
>
> 0 1 0 1
>
> 0 1 0 -1
>
> Contrasts (.mtx files):
> Tp1vsTp2.GrExp0 0 1 0
> Tp1vsTp2.GrControl  0 0 0 -1
> Interaction  0 0 1 -1
>
> Would this design be the correct one to use in this case?
>
> Alternatively, could it be this the correct one?
>
> GroupDescriptorFile 1
>
> Class Subject1
>
> Class Subject2
>
> Variables Tp1vsTp2
>  Groupxtime
>
> Input   Subject1_time1  Subject1 11
>
> Input   Subject1_time2  Subject1-1
> *-1*
>
> Input   Subject2_time1  Subject2 1
> *-1*
>
> Input   Subject2_time2  Subject02   -1  1
>
> Design matrix:
>
> 1 0  1 1
>
> 1 0 -1 -1
>
> 0 1  1 -1
>
> 0 1  -1 1
>
>
>
> Contrasts (.mtx files):
>
> Tp1vsTp20 0 1 0
>
> Groupxtime Interaction   0 0 0 1
>
> Thank you very much in advance.
>
> Kind regards,
>
> Agurne
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
> 
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] Welcome to the "Freesurfer" mailing list {Disarmed}

[fsbuild]

External Email - Use Caution

Hello Nicholas,
Please check you setting for the environment variable FREESURFER_HOME. I 
used the Mac 7.1.1 release package 
fromhttps://secure-web.cisco.com/1UkHJYwewl8qS85O_CWV-J5WUiafp7vGnbHtJ7jYex3q0G5kU2j5BECwnS7n9fZB3i0kvic0yZqcpw3vXMEiw3il7sAIo6rW-Cw5CRPPrvcd7DAQfd2yTTA0tOZNkeKolTGYDuJppsd9Rwtvysyr3s1Jpd6n1TNdrLNouzX5CyNn3BNbOZKSRStOnY9-YQ39TJXtVavlofVBXsduDz3pfUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-darwin-macOS-7.1.1.pkg%C2%A0to
 install freesurfer, so that means after installation FREESURFER_HOME is set as,
$export FREESURFER_HOME=/Applications/freesurfer/7.1.1
 and the ls command outputs …
$ls $FREESURFER_HOMEASegStatsLUT.txt* 
 SetUpFreeSurfer.sh* 
etc/
sources.csh*DefectLUT.txt* 
  
Simple_surface_labels2009.txt*fsafd/  
 
sources.sh*FreeSurferColorLUT.txt*   
WMParcStatsLUT.txt* 
fsfast/
   subjects/FreeSurferEnv.csh*  
   average/
  lib/  
  
tkmeditParcColorsCMA*FreeSurferEnv.sh*
  bin/  
  matlab/  
 
trctrain/Freeview.app/  
  build-stamp.txt*
  mni/  
  
uninstall.sh*SegmentNoLUT.txt* 
 diffusion/  
   python/SetUpFreeSurfer.csh*  
  docs/   
 sessions/
… and shows the SetUpFreesurfer.sh script is there …
Once you have set FREESURFER_HOME and verify with the ls command that you can 
see the SetUpFreesurfer.sh script, then it should work to do,
$source $FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-darwin-macOS-7.1.1-20200726-8b40551 Setting up environment 
for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME/Applications/freesurfer/7.1.1FSFAST_HOME
  /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR  
/Applications/freesurfer/7.1.1/subjectsMNI_DIR  
  /Applications/freesurfer/7.1.1/mni
There are instructions 
athttps://secure-web.cisco.com/1yfyz92Kb9rfbFcHszgMJR0t3oQo4dtacsW4yWoxKnJic0Og6Xuh8TYVutgwwd4ukgaSKh93UQF08nW-hJa89R4ksHO_H641Tmn_2kI2Fr2Qw9Z2f7J6nZlp1BwkWw3kz_VF0XfQKr7GgxwUPVUbh_1rH5fndGG-LjPzbTjKId9Czr5zVqb6meKyYybNBprr4zLjTAMYp2k2pwzo32mOsqw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac%C2%A0under
 the section "Using the Mac Package Installer” about using the installer 
package.
- R.

On Nov 4, 2020, at 22:58, Nicholas BH NG (NUHS) 
nicholas_bh...@nuhs.edu.sg 
wrote:External Email - Use 
CautionDear Free SurferI 
followed the excellent video step by step instructions. At the last part of 
putting the code/ key into the terminal, I encountered the error message as 
below: no such file or directory. As such I think my set up was not 
complete.Kindly advice.Thank youNicholasNicholass-MacBook-Pro:~ Nic$ 
source $FREESURFER_HOME/SetUpFreeSurfer.sh-bash: 
/Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or 
directoryNicholass-MacBook-Pro:~ Nic$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh-bash: 
/Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or 
directoryNicholass-MacBook-Pro:~ Nic$Begin forwarded 
message:From:freesurfer-requ...@nmr.mgh.harvard.eduSubject:Welcome
 to the "Freesurfer" mailing listDate:5 November 2020 at 11:56:45 AM 
SGTTo:nicholas_bh...@nuhs.edu.sgEmail is from external 
source.Do not click on links or open files if unsure of sender..Welcome 
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[Freesurfer] [FreeSurfer] Two Postdoctoral Fellowships in Aging and Alzheimer's disease {Disarmed}

[Hwamee Oh]

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We are seeking two highly motivated postdoctoral researchers to lead
NIH-funded projects in the Laboratory for Cognitive and Translational
Neuroscience directed by Dr. Hwamee Oh at Brown University. One position is
to use fMRI and PET to study visual memory networks in healthy young,
cognitively normal older adults, and older adults who are considered as
preclinical Alzheimer's disease. The other position is to understand the
brain networks that underlie risk and resilience to aging and Alzheimer's
disease in a 60-year longitudinal study cohort.

Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology,
biomedical engineering, or a relevant field are encouraged to apply. Prior
experience with human neuroimaging, a strong background in cognitive
neuroscience and experimental design, and/or familiarity with programming
in relevant languages (e.g., Python, MATLAB) are required.

The expected start date is July 2021 or negotiable. A link to the full
description of the fellowship positions can be found here under "Research
Fellowship Program":
https://secure-web.cisco.com/1OPjthLpBzhYKFTSwjkVOmEIR06WelLxkClkKQkPxS4xR8G-p495UGlW3qF-rPoHu3g1sRlvwBVMIdei1IZAvLDyg3psxXsUk-Fi93fbF5Zq0gA2-EPtYGkk5atfHs70u35Ou7zdMDch-sU5wr641IRKJc3zITrAMJnIAR-yfDMKLX3Z-XBpwLdUamd7j1fXVfDts2ZUDN9_7n5K3vJP_sA/https%3A%2F%2Fwww.brown.edu%2Fclinical-psychology-training%2Fpostdoctoral-fellowship%2Fpostdoctoral-fellowship-applicants%2Favailable-fellowships
.

A deadline for early decision applicants is December 11, 2020, and a
regular decision deadline is January 4, 2021. More details can be found:
https://secure-web.cisco.com/1nI5zbsgp-rII9YGTnQVPZOgDTWuOf1k9XnIzMiA-caXOKNK1mg9g36Ngs7Atv4XF4K7e6shG8tIDbgJ33fVsU1PybL01q7PI50afQpajh00sVCArI_JDLbl6lsnc7y8PbsRF3hSiN-pc7CKTgH0NedOGQTHvk26Bb3DC6e6awqSuxah4mwQso3t3wPWvARc_QwdBth8B_hYoW-5KDbjpJw/https%3A%2F%2Fwww.brown.edu%2Fclinical-psychology-training%2Fpostdoctoral-fellowship%2Fpostdoctoral-fellowship-applicants%2Fapplication
.

Interested applicants are strongly encouraged to email a brief description
of research background and career goals, and CV with a list of 3 references
to Dr. Hwamee Oh at hwamee...@brown.edu.

Contact Website
https://secure-web.cisco.com/1pnx_q2Y5nyTYo0Dg8xD1BekP2g7YWTdX_-COGIFVVfh7ztOeTcBXJiYvW6cZLAdNYKU4LKHgORUrhWmJqDyjqiS_VWogjjVT8qSigzB0zNWckMcAzUPQpAZizTJxZXrEYU5rdfVn_mkCQ1VpF7XD4TimA996tizLcRBRCR8fgLfKLHnKkV2iSy8ufzarTZAkdk57tQb6vQbl-X_1i42qzw/https%3A%2F%2Fsites.brown.edu%2Foh-ctnlab%2Favailable-positions%2F
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Re: [Freesurfer] mri_glmfit_sim error (Douglas N. Greve)

[Basavaraju, Rakshathi]

External Email - Use Caution

Hi Douglas,

This is for a lGI analysis. I used a fwhm of 10 and not 38:

mri_surf2surf --hemi lh --s fsaverage --sval lh.lgi.mgh --fwhm 10 --cortex 
--tval lh.lgi.10B.mgh

So why am I getting this error?
cannot find 
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd
When I run : mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs 
--cwpvalthresh .05 --2spaces??

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: 05 November 2020 11:29
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Freesurfer Digest, Vol 201, Issue 6

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. LGI quality control {Disarmed} (Nelson, Eric)
   2. Re: Meta-analysing brain measure statistics across multiple
  cohorts using different versions of Freesurfer (Stephanie K)
   3. Re: Meta-analysing brain measure statistics across multiple
  cohorts using different versions of Freesurfer (Ammon, William)
   4. Re: aparcstats2table {Disarmed} (Kiyotaka Nemoto)
   5. Fwd: Welcome to the "Freesurfer" mailing list {Disarmed}
  (Nicholas BH NG (NUHS))
   6. Fwd: using CAT12 segmentation for PVC (Donatienne Van Weehaeghe)
   7. aparcstats2table (Saman Fouladi)
   8. Join the Brainhack donostia (Vicente Ferrer)
   9. repeated measures ANOVA 2x2 two groups two times  {Disarmed}
  (Agurne Sampedro Calvete)
  10. Re: .mgh file unknown, GLM paired analysis {Disarmed}
  (Agurne Sampedro Calvete)
  11. Re: mri_glmfit_sim error (Douglas N. Greve)
  12. Re: mri_convert error (Douglas N. Greve)
  13. Re: Extract he value of area and volume in the fsaverage for
  every subject {Disarmed} {Disarmed} (Douglas N. Greve)
  14. Re: Question about smoothing for extracting anatomical stats
  {Disarmed} (Douglas N. Greve)
  15. Re: Troubleshooting -parallel flag for Freesurfer, error in
  the cortical ribbon mask stage during recon-all {Disarmed}
  (Douglas N. Greve)
  16. Re: Fixing error with pial surface {Disarmed} (Douglas N. Greve)
  17. Re: mris_anatomical_stats error: stating file (Douglas N. Greve)
  18. Re: (no subject) (Douglas N. Greve)
  19. Re: Fwd: using CAT12 segmentation for PVC (Douglas N. Greve)
  20. Re: repeated measures ANOVA 2x2 two groups two times
  {Disarmed} (Douglas N. Greve)
  21. Re: LGI quality control {Disarmed} (Douglas N. Greve)
  22. Re: repeated measures ANOVA 2x2 two groups two times
  {Disarmed} (Agurne Sampedro Calvete)
  23. Re: trac-preproc error (Hasimoglu, Yasemin)
  24. Re: mris_anatomical_stats error: stating file (Chan, Shi Yu)


--

Message: 1
Date: Wed, 4 Nov 2020 19:12:50 +
From: "Nelson, Eric" 
Subject: [Freesurfer] LGI quality control {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:



Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Hello,

I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now 
trying to quality check my data using tksurfer as described on the wiki
tksurfer my_subject_id lh inflated -overlay lh.pial_lgi
However the LGI overlay is not covering the entirety of the inflated brain. 
Specifically the medial frontal surface and some subcortical are not measured 
for LGI.  Here is a link of the overlay images for a few subjects: 

Re: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

[Fischl, Bruce]

Hi Lee

It's really hard to say. The change in voxel size might sound trivial, but it 
is a 30% change in volume (and hence SNR). The longer TE will counteract that 
by increasing T2* weighting.
Sorry I don't have anything more conclusive to say except that it is obviously 
not ideal
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Backhausen, Lea
Sent: Thursday, November 5, 2020 12:13 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}


External Email - Use Caution
Dear FreeSurfer experts,

I am currently working on a longitudinal data set with 4 time points, acquired 
at one site with the same Siemens Trio 3T scanner.
Unfourtunately, the T1 sequence differs slightly for one of these time points. 
These sequences have been measured:


  1.  repetition time (TR) = 2300 ms, echo time (TE) = 2.93 ms, inversion time 
(TI) = 900 ms, voxel size = 1.1 x 1.1 x 1.1mm, flip angle = 9°; matrix size = 
256 x 256 x 160 mm
  2.  repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, inversion time 
(TI) = 900 ms, voxel size = 1.0 x 1.0 x 1.0mm, flip angle = 9°; matrix size = 
256 x 256 x 176 mm

Is it possible to process these different sequences in the longitudinal stream 
(if e.g. one participant would have 3 data sets of sequence 1 and one data set 
of sequence 2)?
Or would this cause too much bias?

Thank you very much, kind regards!
Lea Backhausen



--
Lea Backhausen
Ph.D. Student (M.Sc. Psychology/Neuroscience)
Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU 
Dresden, Germany
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.uniklinikum-dresden.de

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[Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

[Backhausen, Lea]

External Email - Use Caution

Dear FreeSurfer experts,

I am currently working on a longitudinal data set with 4 time points, acquired 
at one site with the same Siemens Trio 3T scanner.
Unfourtunately, the T1 sequence differs slightly for one of these time points. 
These sequences have been measured:


1)  repetition time (TR) = 2300 ms, echo time (TE) = 2.93 ms, inversion 
time (TI) = 900 ms, voxel size = 1.1 x 1.1 x 1.1mm, flip angle = 9°; matrix 
size = 256 x 256 x 160 mm

2)  repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, inversion 
time (TI) = 900 ms, voxel size = 1.0 x 1.0 x 1.0mm, flip angle = 9°; matrix 
size = 256 x 256 x 176 mm

Is it possible to process these different sequences in the longitudinal stream 
(if e.g. one participant would have 3 data sets of sequence 1 and one data set 
of sequence 2)?
Or would this cause too much bias?

Thank you very much, kind regards!
Lea Backhausen



--
Lea Backhausen
Ph.D. Student (M.Sc. Psychology/Neuroscience)

Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU 
Dresden, Germany
http://secure-web.cisco.com/1uRUN3qw4_2ZQdVovG97ElQWo_5ofjkray9cxFwmREkCPYfVKmkg3mCWoPyBs1HqluQDi-T-0PAG9qvZspvxnt5cexmdXyZnGWTOw-97vp9_hXAC2oIBhA293ZZxuiURC96CETYYfNyhCOBNbTO1VHV6RbKDi6vXA9Xh3lW5EjpWfrYXJqBIjofhGIZBip556JpEIC432Q_E9v-wyIawKIA/http%3A%2F%2Fwww.uniklinikum-dresden.de

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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

[Donatienne Van Weehaeghe]

External Email - Use Caution

The subcortical structures were not delineated correctly, especially the
nucleus caudatus which had a lot of atrophy in this particular patient
group.

Kind regards
Donatienne

Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve :

> I don't think CAT creates white or pial surfaces, so no. What is wrong
> with your FS analysis?
>
> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
> Dear,
>
> The segmentation using Freesurfer was incorrect, however we have a good
> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer?
>
> Kind regards
> Donatienne
>
> ___
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>
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Re: [Freesurfer] mris_anatomical_stats error: stating file

[Chan, Shi Yu]

Hi,

Yes, sorry! I copied the error message from terminal, but copied the command 
from my script so I copied the error message for the wrong hemisphere. I 
apologise for the confusion.

I've attached the terminal output (I've put # at the lines above the error 
message) and the script I use in this email.

Thank you for all your help!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, November 5, 2020 9:44 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file


Is that the right error msg? It says it can't find the RH, but you are running 
it with LH. Can you post the entire terminal output?


On 11/3/2020 2:00 PM, Chan, Shi Yu wrote:

Hi FreeSurfer Developers,


I'm trying to calculate cortical thickness statistics from the Yeo 17 Network 
cortical parcellation and have used mri_surf2surf to get the .annot files for 
each subject.


However, when I run mris_anatomical_stats, I get an error:


ERROR: stating file 
subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot


It seems like the "sub-001/label" portion is repeated.


The command I use for mris_anatomical_stats is:


mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f 
sub-001/stats/lh.Yeo_17Networks.stats -b -a 
sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white


The command still runs despite the error, and outputs the stats files 
accordingly, so I'm not sure how important this error is, but I can't figure 
out how to fix it.


This is a similar issue to: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html but 
I've checked $SUBJECTS_DIR, and it is correct. If I run ls 
$SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri 
stats labels etc)



Any help would be much appreciated! Thank you!




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PHS009090:freesurfer pnlmcleaneeg$ bash extractYeo17.sh
/Volumes/SY_MRI/freesurfer/recon_unedited
sub-001_ses-01
Setting mapmethod to nnf

7.1.1

setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh 
--sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
 

sysname  Darwin
hostname PHS009090
machine  x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype= 
trgsubject = sub-001_ses-01
trgval = 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.sphere.reg
Loading source data
Reading surface file 
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.orig
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Reading target surface reg 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (134953)

Surf2Surf: Dividing by number of hits (134953)
INFO: nSrcLost = 0
nTrg121 = 134953, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 1, nSrcLost = 0, nSrcMulti = 10241, MnSrcMultiHits = 13.1776
Saving target data
Converting to target annot
Saving to target annot 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
Setting mapmethod to nnf

7.1.1

setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh 
--sval-annot 
fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
 

sysname  Darwin
hostname PHS009090
machine  x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype= 
trgsubject = sub-001_ses-01
trgval = 
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 

Re: [Freesurfer] trac-preproc error

[Hasimoglu, Yasemin]

Hi Anastasia,

I uploaded the files. Let me know if you have trouble viewing them!

Best,
Yasemin

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, November 2, 2020 10:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] trac-preproc error

Hi Yasemin - If you upload all the tracula output files for me here, I'll take 
a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/

Please include all the output directories for this one subject in one zip file. 
Thanks!

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hasimoglu, Yasemin 

Sent: Thursday, October 29, 2020 11:47 AM
To: Freesurfer support list 
Subject: [Freesurfer] trac-preproc error

Hi,

I'm running Tracula on a longitudinal dataset and it's failing at the preproc 
stage for one subject with the following message:

INFO: Distances between consecutive points in test subject's space are 16 13 12 
14
WARN: Could not find satisfactory control point fit - try 4967
Finding center streamline
INFO: Step is 3 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 3 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 3 voxels
WARN: Turning off overlap check for center streamline
INFO: Step is 3 voxels
WARN: All checks already off. Exiting.
Selecting 5 points on center streamline
ERROR: Selected streamline has fewer than 5 points
Linux zorii.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Oct 28 04:11:51 EDT 2020

It looks like the problem is with one specific pathway. I checked the brainmask 
and the inter and intra-subject registrations and they all look fine to me, so 
I'm not sure what else to check. The trac-all.log file is quite large, I 
attempted to attach it in this email several times, but it always gets 
rejected, so I'm not attaching it for now. I would greatly appreciate any 
advice!

Best,
Yasemin
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Re: [Freesurfer] LGI quality control {Disarmed}

[Douglas N. Greve]

When you click on the gray areas, is the value 0 or just something very 
close to 0? You may need to set the lower threshold (default is 2). 
Also, I would recommend using freeview via tksurferfv (same command line 
as tksurfer)


On 11/4/2020 2:12 PM, Nelson, Eric wrote:


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Hello,

I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. 
I am now trying to quality check my data using tksurfer as described 
on the wiki


/tksurfer my_subject_id lh inflated -overlay lh.pial_lgi/

However the LGI overlay is not covering the entirety of the inflated 
brain. Specifically the medial frontal surface and some subcortical 
are not measured for LGI.  Here is a link of the overlay images for a 
few subjects: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.dropbox.com/s/9pt8rti4yjudrza/LGI_QC.png?dl=0. I 
. 
I haven’t been able to find any images of what this overlay should 
look like so I don’t know if this is expected or if something has gone 
wrong with the processing. Any feedback would be greatly appreciated


Best,

Eric


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Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed}

[Agurne Sampedro Calvete]

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Dear FS experts,

I have removed the backslashes "\" and now it works, so problem solved.

Thank you very much.

Regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (<
a.sampe...@deusto.es>) escribió:

> Dear Freesurfer Experts,
>
> I am trying to perform a paired analysis in FreeSurfer following this
> tutorial 
> https://secure-web.cisco.com/1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpeOEgVTUnDNdXv_pENZI_Zj8E1pQJo1vbndz8QuwfXZeLFZrg8uFaXPMF0SqFXPUHmLNodW7Jl-SXS-ePsn2uN1wrgmWAb4tMFpdB1JokGuLZFVIqK_lmBvM7eufXwSmiMuSvGQ2NREwZt2mxapAyIqfuj9JwrJS-MUE9Nm4DNw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
>  and I
> have some problems when running the spatially smooth.
>
> I ran the following command:  mri_surf2surf --s fsaverage --hemi lh --fwhm
> 5\ --sval lh.paired-diff.thickness.mgh \ --tval
> lh.paired-diff.thickness.sm05.mgh
>
> And I found this error:
> ERROR: lh.paired-diff.thickness.mgh unknown freesurfer
>
> This file is in my subject directory, but when I see the file properties,
> in the "file type" box it says: unknown. I have read that other users have
> experienced the same error.
>
> What can I do to solve this problem?
>
> Thanks in advance.
>
> Kind regards,
>
> Agurne Sampedro
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
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Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Douglas N. Greve]

In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer 
your question, the first example you give is the right way to handle it.



On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:


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Dear Freesurfer experts,

I am trying to do a longitudinal repeated measures ANOVA 2x2, with two 
groups (experimental vs control) and two time points (pre and post 
treatment).


Although I have run a paired t-test, now I would like to do a repeated 
measures anova 2x2, since I am doing the same analyses with other data 
in other softwares.


I am trying to follow the tutorial *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova 
, 
but I have several doubts when designing the FSGD file as well as the 
contrasts.


How should it be the FSGD file?

I have seen in a previous post the following design for the same 
number fo groups and time points:


GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2.GrExp 
   Tp1vsTp2.GrControl


Input   Subject1_time1  Subject1 
1 0


Input   Subject1_time2  Subject1    
-1    0


Input   Subject2_time1  Subject2 0 1

Input   Subject2_time2  Subject02  
 0 -1


Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1


Contrasts (.mtx files):
Tp1vsTp2.GrExp        0 0 1 0
Tp1vsTp2.GrControl  0 0 0 -1
Interaction 0 0 1 -1

Would this design be the correct one to use in this case?

Alternatively, could it be this the correct one?

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2 
 Groupxtime


Input  Subject1_time1  Subject1 1    1

Input  Subject1_time2  Subject1 -1 *-1*

Input   Subject2_time1  Subject2   1 *-1*

Input  Subject2_time2  Subject02  -1  1

Design matrix:

1 0  1 1

1 0 -1 -1

0 1  1 -1

0 1  -1 1

Contrasts (.mtx files):

Tp1vsTp2 0 0 1 0

Groupxtime Interaction   0 0 0 1


Thank you very much in advance.

Kind regards,

Agurne

Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es 



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC

[Douglas N. Greve]

I don't think CAT creates white or pial surfaces, so no. What is wrong 
with your FS analysis?


On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:


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Dear,

The segmentation using Freesurfer was incorrect, however we have a 
good segmentation from Cat 12. Can we use this segmentation for PVC in 
PETsurfer?


Kind regards
Donatienne

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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Try this instead
aparcstats2table --hemi lh  --subjects subj10 --parc aparc.a2009s  
--meas meancurv --tablefile /home/team33/ aparcstats.txt


On 11/3/2020 12:20 PM, saman fouladi wrote:


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hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats 
--parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ 
aparcstats.txt

"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me




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Re: [Freesurfer] mris_anatomical_stats error: stating file

[Douglas N. Greve]

Is that the right error msg? It says it can't find the RH, but you are 
running it with LH. Can you post the entire terminal output?



On 11/3/2020 2:00 PM, Chan, Shi Yu wrote:


Hi FreeSurferDevelopers,


I'm trying to calculate cortical thickness statistics from the Yeo 17 
Network cortical parcellation and have used mri_surf2surf to get the 
.annot files for each subject.



However, when I run mris_anatomical_stats, I get an error:


ERROR: stating file 
subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot



It seems like the "sub-001/label" portion is repeated.


The command I use for mris_anatomical_stats is:


mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label 
-f sub-001/stats/lh.Yeo_17Networks.stats -b -a 
sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white



The command still runs despite the error, and outputs the stats files 
accordingly, so I'm not sure how important this error is, but I can't 
figure out how to fix it.



This is a similar issue to: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html 
 but 
I've checked $SUBJECTS_DIR, and it is correct. If I run ls 
$SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in 
sub-001 (mri stats labels etc)


Any help would be much appreciated! Thank you!



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Re: [Freesurfer] Fixing error with pial surface {Disarmed}

[Douglas N. Greve]

Try these instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 11/3/2020 12:38 PM, Julie Ottoy wrote:


External Email - Use Caution

Hi Bruce,

Thanks for your answer and cc'ing Rob.
I did use anonymous as the username.

Thanks,
Julie

On Tue, 3 Nov 2020 at 11:44, Fischl, Bruce > wrote:


Hmmm, did you log in as anonymous? I’ll cc Rob who should be able
to help

Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Julie Ottoy
*Sent:* Tuesday, November 3, 2020 11:12 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Fixing error with pial surface {Disarmed}

*External Email - Use Caution *

Hi Bruce

Thank you!

Meanwhile, I tried to upload the subject on the server but I
always get the following error:

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put subject_FS_upload.zip
local: subject_FS_upload.zip remote: subject_FS_upload.zip
421 Service not available, remote server has closed connection

Could you help me out with this?

Thanks

Julie

On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:

Hi Julie

It’s really hard to diagnose this way. Are you able to upload
the subject? If so, please send us the coordinates of the
region where you think things are going wrong

Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Julie Ottoy
*Sent:* Monday, October 12, 2020 3:42 PM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Fixing error with pial surface

*External Email - Use Caution *

Hi Bruce,

Thanks for your answer. I have checked the wm.mgz but it does
not seem to be a topological error I think.

I have added coronal, axial, and sag views in attachment (see
the red cursor). Also I have added the first (coronal) slice
that starts to show white matter (couple slices later).

Let me know if you still would like me to upload the data.

Best

Julie

On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:

Hi Julie

It’s hard to tell from the single slice. Is there white
matter in the wm.mgz that doesn’t have surface (?h.white)
covering it? That would indicate a topological defect.


If you upload the entire gzipped and tarred subject’s
directory we will take a look

Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On
Behalf Of *Julie Ottoy
*Sent:* Sunday, October 11, 2020 3:51 PM
*To:* Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Fixing error with pial surface

*External Email - Use Caution *

Dear Freesurfer team,

I have a question related to fixing the pial surface when
a part was missed (see attachment). On the freesurfer
website, I only found how to erase the pial when there was
too much (see *MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0


), but I could not find what to do when there was too little.

As there is no white matter in this particular area, it is
also not an option to place control points. Also the skull
stripping 

Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed}

[Douglas N. Greve]

Hi Andy, this is a bug introduced in 7.1.1, some kind of race condition.
You can fix it by commenting out this line in recon-all
  if($OMP_NUM_THREADS > 1 && ! $LHonly && ! $RHonly) set cmd = ($cmd 
--parallel) # just hemis

doug



On 11/3/2020 12:06 PM, Andy Worth wrote:


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Hello,

We've experienced random crashes when using the -parallel flag with 
the official FS docker container at *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://hub.docker.com/r/freesurfer/freesurfer/ 
.  
It looks like this issue: *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67588.html 
.


Is there a fixed recon-all that I can use with that image (or maybe a 
new image coming soon)?


Thanks,
Andy Worth
Scientific Solutions Engineer
he, him, his


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Re: [Freesurfer] Question about smoothing for extracting anatomical stats {Disarmed}

[Douglas N. Greve]

This is not needed or recommended. Not needed because you are already 
averaging over space and not recommended because it would cause one 
region to bleed over into another.


On 11/3/2020 7:00 AM, Hye Min Shin wrote:


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Hello experts,

So I understand that when doing mri_glmfit you want to use smoothed 
surface maps to comply with random field theory while controlling for 
multiple comparisons (as discussed here: *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67902.html 
). 



But I was also wondering whether we have to smooth surface maps when 
using mri_anatomical_stats to extract anatomical measurements? I see 
that mri_anatomical_stats has the option to smooth by # of iterations 
but is there a way to know how many # of iterations would equal let's 
say 15 FWHM?


Best,
Julia Shin

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Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed}

[Douglas N. Greve]

Try
--slabel fsaverage lh /path/to/lh.areapial.label

On 11/2/2020 10:24 PM, 李梦君 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？


-原始邮件-
*发件人:*"Douglas N. Greve" 
*发送时间:*2020-11-02 23:36:14 (星期一)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* 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, 李梦君 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


-原始邮件-
*发件人:*"Douglas N. Greve" 
*发送时间:*2020-10-30 23:40:30 (星期五)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* 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, 李梦君 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] mri_convert error

[Douglas N. Greve]

It looks like it is trying to extract diffusion info. Try running it 
with --no-dwi


On 11/2/2020 5:11 PM, Georgina Angelopoulou wrote:


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Dear Freesurfer Developers,

I am sorry I did not include the error message.
I am attempting to convert some dicom files to mgz via mri_convert 
command. However, for only 5 participants from my cohort I get the 
following error.

Could you please help me to resolve the problem?

(base) Georgias-MBP:HC21 georgina$ mri_convert 
1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz
mri_convert.bin 
1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm...
Starting DICOMRead2()
dcmfile = 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm

dcmdir = /Users/georgina/Downloads/HD/HC21
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm

break DICOMRead.c:5228
Ref Series No = 201
Found 172 files, checking for dicoms
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm

break DICOMRead.c:5228
First Sorting
Computing Slice Direction
Vs: -0.99478 0.102 0.0033
Vs: -0.994779 0.102 0.0033
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 82
ndcmfiles = 82
PE Dir =  (dicom read)
CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could 
not open file

Too many open files
ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt
Loading pixel data
ERROR: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm 
is not a dicom file

70092 Requested element (18 9089) not found in DCM_GetElementVM


Thank you in advance,
Georgina


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Re: [Freesurfer] mri_glmfit_sim error

[Douglas N. Greve]

Information about multiple comparisons correction has been pre-computed 
for various parameters, including the FWHM. In this case, the measured 
FWHM (38) is outside of the precomputed range. 38 is extremely high. Is 
this a thickness study? What smoothing level did you apply (--fwhm in 
mri_glmfit)?




On 11/2/2020 2:22 PM, Basavaraju, Rakshathi wrote:


External Email - Use Caution

Hi all,

I ran a multiple comparison correction for a surface based analysis 
with this command:


mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh 
.05 --2spaces


But I am getting the following error:

cannot find 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd


What might this error mean? I searched in the mail archives but could 
not get any proper answer. Kindly help me.


Thanks


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[Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to do a longitudinal repeated measures ANOVA 2x2, with two
groups (experimental vs control) and two time points (pre and post
treatment).

Although I have run a paired t-test, now I would like to do a repeated
measures anova 2x2, since I am doing the same analyses with other data in
other softwares.

I am trying to follow the tutorial
https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova,
 but I have
several doubts when designing the FSGD file as well as the contrasts.

How should it be the FSGD file?

I have seen in a previous post the following design for the same number fo
groups and time points:

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2.GrExp
   Tp1vsTp2.GrControl

Input   Subject1_time1  Subject1 1 0

Input   Subject1_time2  Subject1-10

Input   Subject2_time1  Subject2 0
1

Input   Subject2_time2  Subject02   0 -1



Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1

Contrasts (.mtx files):
Tp1vsTp2.GrExp0 0 1 0
Tp1vsTp2.GrControl  0 0 0 -1
Interaction  0 0 1 -1

Would this design be the correct one to use in this case?

Alternatively, could it be this the correct one?

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2
 Groupxtime

Input   Subject1_time1  Subject1 11

Input   Subject1_time2  Subject1-1
*-1*

Input   Subject2_time1  Subject2 1
*-1*

Input   Subject2_time2  Subject02   -1  1

Design matrix:

1 0  1 1

1 0 -1 -1

0 1  1 -1

0 1  -1 1



Contrasts (.mtx files):

Tp1vsTp20 0 1 0

Groupxtime Interaction   0 0 0 1

Thank you very much in advance.

Kind regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
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[Freesurfer] Join the Brainhack donostia

[Vicente Ferrer]

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The Basque Center on Cognition, Brain and Language (BCBL) is holding a free 
online next week. We hope that it can be of interest to this community, and 
that you could forward others this information.

At the BCBL, we are organizing the third edition of Brainhack Donostia 
(https://secure-web.cisco.com/1GC1hh4vsRCGfthBadagfSojiEis8P2rIcxlvHWMBmSe1mUpZN3XGoyqUkNT24qIKWA4N8W1cAJhN_7ft-aQLlYJIb0H8TlsJ9S54qyypnyL1ycUZHdN3oJG0eaekXVHXHFEXOi0PDEQBEuw2jFVaDaDUYvE_7MLqarw_3M7j-hxsrsF9Y7THetqI-Q1Ea-zdxXCdhCXqEkCdMwHY5Wtj2A/https%3A%2F%2Fbrainhack-donostia.github.io),
 an event focused on neuroscience and the promotion of open-source resources in 
an accessible way across disciplines and experience levels.

This year's edition is taking place from November 9 through November 13: it 
will be held online and will be completely free. The focus of BHD2020 will be 
OpenScience, covered from a variety of pertinent perspectives (e.g., MEG, fMRI 
and fNIRS). We are going to have the cream of the crop as invited speakers, 
check the schedule here: 
https://secure-web.cisco.com/1nN_lXzurOj1ntsI3lbjeAWTurwndamZGsnyiXQE9Xqhw7ivPBzYGFR4-RAqIVlVWDs96ck1xVRomqnOIgkrdtL0kUMVfuhPq_2aalh5CMTkP3S7VKCbuF0UbbhqJVXFJW-MFeH45x1Us-vPHABKO2RgJMyuWyV4cdUeEGJEWw7WiIrllUoN98LCI-d4ormPXudSRhw-XF0TPSqL-jO8n9A/https%3A%2F%2Fbrainhack-donostia.github.io%2Fschedule%2F.

Even though we will be physically distant, there will be the possibility to 
come together and socialize on the Brainhack Donostia GatherTown platform. We 
will be using the platform to host exciting social activities throughout the 
event. Stay tuned for the social activities program!

We invite all neuroscience aficionados, students of neuroscience-related 
subjects, professors and professionals to participate. Registrations are now 
open at 
https://secure-web.cisco.com/1d3VTvJ1ukmPmrYp15NgAyjM96L0VJDHuND2s9vyXzTZc5kij6rj_8FjmimUU-ATDmbz31T5ZunN4ZMQuKhA2L9S_tJaf2RH_5JCuyO9GbyUeRTL0vUAJ5mfA_GF3aX8OcrtT2CYADu6DC5fDjAeKMTDIP59_wf8oIQESZzt3nOUXJ3NQWOcCy0pKuYDq0_io8yIr_izuOWbBI2TGCcIPyA/https%3A%2F%2Fbrainhack-donostia.github.io%2Fregistration%2F.

Best regards,

Vicente Ferrer
Predoctoral Researcher BCBL
http://secure-web.cisco.com/12Abv6l6_PtwWS0hk38LzFrcDpN7GEtPA16QooQuy_XnRh0GP6GkjqGbuaF9k6hrtOi69W3U7Gt8aSCjj1a0Fh21L9w3pz3iNFEkY67rrKLurTsMS1LoDQmBHIYo73yygeu1xH5QXTdKVorwcucifZx3HuXjAN0PRiUy6wqsvRDpc9KVRjNFU9XCPbqZGA3ZvAqFBuDLyPPMU8MotUZG5Zw/http%3A%2F%2Fwww.bcbl.eu

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[Freesurfer] aparcstats2table

[Saman Fouladi]

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 hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats
--parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats
.txt
"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me
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