[Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

[Hiersche, Kelly J.]

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Hello FreeSurfer Developers,

First, I am new to using Freesurfer, so I apologize if any information is 
unclear.

I am attempting to use the following tutorial 
https://secure-web.cisco.com/1KKgvfrXJGjQJ5zjq_uJgVI7FZF_1Yms747_s_N5YKZgNCGOMeS-uBP8-XyfvGQqxNQ2kNRGpMdVD-l4SP5CiEic9c_tI35GMoJE6Sb491sj-H31iaM-POIUms_Q0s7FHOD2YRT1S9f6rjulYbuOUBL9xxRNRhcK19SgzXAbUPJCM_zmItcZr7pBo3wqHy7IvkxPcZUHHu2qSGURpFsZtpoev0-WE5zGzv7gV_gSisXAPLRyzOFnS-FUhNnf6WkJ4aDshlD1YgdAFvaSof0Q7EdzgPMmTsek__sdyr7qIcKRNn3Vl3g6ARaRHDXMvSsFsesmqvIgyBJKDX-8AWaifiQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastFirstLevel
 to do a surface based GLM in an individual subject (using my own data, not the 
tutorial data), but I am getting the following error:

Error using MRIread (line 76)
ERROR: cannot determine format of
/subnum/bold/runnum/masks/fmcpr.brainmask.fsaverage.lh
(MRIread)

I am getting that error because the fmcpr.brainmask.fsaverage.lh does not 
exist. To fix this error, I re-ran preprocessing using the following tutorial: 
https://secure-web.cisco.com/1R3ca-_kZlKG6UMHW-K0XesdEmNb2A3RSqg26YdNzjZ-RhqmPe-x1ag2VCykMD2zftJadwRyd02YgL1xqEuuo5BSxT6PCdIkNNWUylmMkbaDnk6thb22V1RZQKgXY4xp_r3V7CQ5srW_gt2Lr7hQ3XVEReDCipXQQhcYb6EoCKwknBoPDp0kLj2UL7t85-F8m-Bm2lTwCm4H3QNBdErXl7_KaiEN9_ZYzyU44xXnkEY1MgoXenRnSyLkm2TozNiCMkxQSw2HtBjFstXLvSOFjamEwyooDK2Xv3_t3o_UfyclzKzBt055kbDZw2bp9XBHBGcGhs3ARdDmpbjaNl4atow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastPreProc

After preprocessing, I still got the same error.

Here are the files that do exist in that path: subnum/bold/run-num/masks
brain.e3.nii.gzbrain.fsaverage.lh.pr.nii.gz  
brain.fsaverage.rh.pr.nii.gz  brain.mni305.2mm.pr.nii.gz  
brain.nii.gz.mkbrainmask.log
brain.fsaverage.lh.nii.gz  brain.fsaverage.rh.nii.gz 
brain.mni305.2mm.nii.gz   brain.nii.gz

There are some fmcpr files in this folder: subnum/bold/run-num
fmcpr.brainmask.norm.2x2x2.nii.gz fmcpr.mcdat fmcpr.norm.nii.gz 
 fmcpr.sm5.fsaverage.rh.nii.gz
fmcpr.brainmask.normtmp.2x2x2.nii.gz  fmcpr.nii.gzfmcpr.sm0.norm.nii.gz 
 fmcpr.sm5.mni305.2mm.nii.gz
fmcpr.mat.aff12.1Dfmcpr.nii.gz.mclog  
fmcpr.sm5.fsaverage.lh.nii.gz  fmcpr.sm5.norm.nii.gz


Here are the commands I am running:

These commands work:
mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage 
$hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions 
$nconditions -mask $func_stem.brainmask -gammafit 2.25 1.25 -nuisreg mcprextreg 
6 -TR 1. -polyfit 1 -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude 
$tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run

mkcontrast-sess -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -contrast Con1-Con2 
-a 1 -c 2

preproc-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage lhrh 
-mni305 -fwhm 5 -per-run

This command errors
mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage 
$hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions 
$nconditions -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1. -polyfit 1 
-analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM 
-tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run


  1.  I am running freesurfer through matlab on the Ohio Supercomputer; 
freesurfer/6.0.0

Thank you for all your troubleshooting help!

Kelly

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[Freesurfer] Basic question

[Rosalia Dacosta Aguayo]

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Dear Freesurfer team,

I know this is a basic question, but I would like to be sure before
proceeding. Are those statements below right?

For cortical thickness, I should covariate for age and sex

For volume, I should covariate only for TBV

Thank you for your time and your patience.

Best wishes,
Rosie
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Re: [Freesurfer] Basic question

[Fischl, Bruce]

Hi Rosie

It really depends on what your hypotheses are, but if you are covarying for age 
and gender in thickness you probably want to do so in an analysis of volume as 
well. The only real difference are (1) thickness doesn’t really need TBV 
covariation, and (2) thickness is a more localizable quantity than volume. Of 
course they are different neurobiologically as well, but from an analysis 
standpoint those are the two big differences
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rosalia Dacosta Aguayo
Sent: Sunday, November 21, 2021 1:42 PM
To: Freesurfer support list 
Subject: [Freesurfer] Basic question


External Email - Use Caution
Dear Freesurfer team,

I know this is a basic question, but I would like to be sure before proceeding. 
Are those statements below right?

For cortical thickness, I should covariate for age and sex

For volume, I should covariate only for TBV

Thank you for your time and your patience.

Best wishes,
Rosie


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Re: [Freesurfer] Basic question

[Rosalia Dacosta Aguayo]

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Hi Bruce,

Thank you very much for your answer.

Kind regards,
Rosie




On Sun, Nov 21, 2021 at 8:04 PM Fischl, Bruce 
wrote:

> Hi Rosie
>
>
>
> It really depends on what your hypotheses are, but if you are covarying
> for age and gender in thickness you probably want to do so in an analysis
> of volume as well. The only real difference are (1) thickness doesn’t
> really need TBV covariation, and (2) thickness is a more localizable
> quantity than volume. Of course they are different neurobiologically as
> well, but from an analysis standpoint those are the two big differences
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Sunday, November 21, 2021 1:42 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Basic question
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer team,
>
>
>
> I know this is a basic question, but I would like to be sure before
> proceeding. Are those statements below right?
>
>
>
> For cortical thickness, I should covariate for age and sex
>
>
>
> For volume, I should covariate only for TBV
>
>
>
> Thank you for your time and your patience.
>
>
>
> Best wishes,
>
> Rosie
>
>
> ___
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Re: [Freesurfer] TRACULA configuration file for bash

[Yendiki, Anastasia]

Hi Luis - Not sure if you've tried this already, but the instructions on the 
wiki should work regardless of what your default shell is, because trac-all 
will source the configuration file from within a c shell.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alvarado,Luis R 

Sent: Sunday, October 31, 2021 5:24 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA configuration file for bash


External Email - Use Caution

External Email - Use Caution

Hi FS and TRACULA experts,

I have a simple question. Do I need to replace:


setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs

with:


export SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs

inside the TRACULA configuration file, if my shell is bash? or should I leave 
that alone?

Best,



Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202
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Re: [Freesurfer] Tracula 7.2 using older structural outputs

[Yendiki, Anastasia]

Hi Jim and Luis - The only change between versions of recon-all that would mess 
things up for TRACULA would be if the IDs of the structures in the aparc+aseg 
changed (e.g., the left thalamus changed from 10 to 100) or a new structure got 
added to the aparc+aseg that wasn't there in the previous version or a 
structure got removed. As far as I know, this hasn't happened (the recon-all 
crew can correct me if I'm wrong). So using the output from an older version of 
recon-all when running a newer version of trac-all should be fine.

Since we now also recommend the thalamic nuclei segmentation for the latest 
version of TRACULA (when tracts that terminate or neighbor the thalamus are of 
interest), as Jim said you can always just run the thalamic nuclei segmentation 
on top of your existing recon-all output.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alvarado,Luis R 

Sent: Sunday, October 31, 2021 6:22 AM
To: Freesurfer support list ; 
dimitriosalexopou...@wustl.edu 
Subject: Re: [Freesurfer] Tracula 7.2 using older structural outputs


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Hi all,

I am also curious about this question.

Can you run TRACULA 7.2 using the outputs from FS 6.0 and 7.1.1?

If so, is it ok to run the new segmentThalamicNuclei.sh and segmentBS.sh 7.2 
scripts on FS 6.0 recon data and feed that to TRACULA 7.2?

Best,


Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


From: Alexopoulos, Dimitrios 
Sent: Tuesday, August 24, 2021 2:00 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula 7.2 using older structural outputs


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HI,



Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 
and 7.1.1?



Jim







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[Freesurfer] Requesting to clarify doubts on data analysis

[Koustav Chatterjee]

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Dear FreeSurfer team,

I have a few questions to clarify the confusion regarding data analysis.

   1. For each subject, is it recommended to normalize the raw volumetric
   data by total intracranial volume? If so, is it true only for volumes of
   subcortical structures or, both subcortical and cortical structures?
   2.  In the same way, do I suppose to normalize


   - Different cortical thickness with mean cortical thickness
   - Cortical surface area with total surface area
   - Different cortical curvature with mean cortical curvature

Thank you for your time and help.

Regards,
KC
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Re: [Freesurfer] Pipeline errors - matlab

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

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Hello Eugenio,

Thank you so much for your response. Here is a large section of the error
message I got while running hippocampal subfields. Please let me know if
more details are needed!


**
*   Segmentation violation detected at Fri Nov 12 14:26:43 2021*
**

*Configuration:*
*  Crash Decoding : Disabled*
*  Current Visual : Quartz*
*  Default Encoding   : ISO-8859-1*
*  MATLAB Architecture: maci64*
*  MATLAB Root: /Applications/freesurfer/MCRv84*
*  MATLAB Version : 8.4.0.150421 (R2014b)*
*  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug
30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64*
*  Processor ID   : x86 Family 6 Model 85 Stepping 4, GenuineIntel*
*  Software OpenGL: 0*
*  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode*
*  Window System  : Quartz*

*Fault Count: 1*


*Abnormal termination:*
*Segmentation violation*

*Register State (from fault):*
*  RAX =   RBX = *
*  RCX =   RDX = *
*  RSP =   RBP = *
*  RSI =   RDI = *

*   R8 =    R9 = *
*  R10 =   R11 = *
*  R12 = 7c6edd00  R13 = 7fff203e54bd*
*  R14 = 7fff87147d38  R15 = 7c6edda0*

*  RIP = 3002  RFL = 7f9f5ca7bc80*

*   CS =    FS =    GS = 00010a6d1560*

*Stack Trace (from fault):*
*[  0] 0x00010a320e64
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052*
*[  1] 0x00010a324a2a
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562
_ZN2fl4test17terminate_handledEv+0906*
*[  2] 0x00010a324477
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119*
*[  3] 0x00010dcd9b7a
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962
_Z32mnRunPathDependentInitializationv+3146*
*[  4] 0x00010dcd9e58
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696
_Z32mnRunPathDependentInitializationv+3880*
*[  5] 0x00010dcd7733
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675
mnFatalSignalHandler+0275*
*[  6] 0x7fff20465d7d
 /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029*
*[  7] 0x
 +*
*[  8] 0x000107d7e6ca
/Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178
_ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+0186*


*If this problem is reproducible, please submit a Service Request via:*
*
http://secure-web.cisco.com/1sFp6ev4em_EM8c3cbPoUE6trXNZE7Efoemg6n7hk6C5IFGAsAMrbbI93SRSR8goYyCUFBY68NYUCsB2ph7cj5aHUrjym28U5j03Gc9dH1qdpLKkKkTVKbZ0E3qVZh9N7uZnkk6meV4_HRjZYlsfzCPOW28OcmRDRsqp_jlQVoJSNMFJACs9sJU6zytyTlb2wQYtDc5vOylv5fqJpLgVgRfBV3RmkgQoO7Rsh8PFHHrJ3oiXFc8OSZfFyOmbJfqyMYh0z1EsxQjZjbDinL21loMrMtfRUYB5ATo6Zo5zQW81mGOqsL0ff8TBFoUk5iEiS53q7767J0edrOObAVLjtNj-uXtcriQ3BOeUlYHY9sxE/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
*

*A technical support engineer might contact you with further information.*

*Thank you for your help.** This crash report has been saved to disk as
/Users/ajobsaid/matlab_crash_dump.7498-1 ***


*Caught "std::exception" Exception message is:*
*FatalException*

**
*  std::terminate() detected at Fri Nov 12 14:26:43 2021*
**

*Configuration:*
*  Crash Decoding : Disabled*
*  Current Visual : Quartz*
*  Default Encoding   : ISO-8859-1*
*  MATLAB Architecture: maci64*
*  MATLAB Root: /Applications/freesurfer/MCRv84*
*  MATLAB Version : 8.4.0.150421 (R2014b)*
*  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug
30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64*
*  Processor ID   : x86 Family 6 Model 85 Stepping 4, GenuineIntel*
*  Software OpenGL: 0*
*  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java
HotSpo

Re: [Freesurfer] Pipeline errors - matlab

[fsbuild]

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The Matlab MCRv84 release used by Freesurfer is too old to be supported on 
MacOS 11 Big Sur by The Mathworks (looks like you are running MacOS 11.5 beta 2 
release).
There are also error reports similar to yours with old versions of Matlab on 
different versions of MacOS.  From what I read on The Mathworks web site, 
it looks like a fix was made in R2017b, but I don’t if that release will work 
with freesurfer or MacOS 11.
If you want to try that release, you could do the following.
Download R2017b 
from,https://secure-web.cisco.com/1cphCEkfouFma1YYMWmPUTPpDCt3HnegC93vKeXgpXkYopaRmrIFAOX5SsTtI6kXwY57rQFCzCky19jtT-4kLesJXahLsC0dpNHkWy95k1whjdSQIL25rYQTwYN5GqmohnATiCOl3zc0iNbjFqu_1GG674YhHdBYM71d8D0WvsPlqT47FNblY-U2xxXfcogMV8EB_aZXY5lzxSMUsQqK_Gm_EyYoxPeyS0tq4_qT5joqonK1Hd5O-IPookdc4hztXvq7Kufv6wm4j3NICs58RMrcnTR644b2VW43sg_31wMfxVN9TXnBcP61uW1gNDJvUjN0UlZCiJlg3j5A4WAXC_qWVNGGyXAn_uCKuns3eKf8/https%3A%2F%2Fssd.mathworks.com%2Fsupportfiles%2Fdownloads%2FR2017b%2Fdeployment_files%2FR2017b%2Finstallers%2Fmaci64%2FMCR_R2017b_maci64_installer.dmg.zip
After downloading, double click on the zip archive to get the dmg 
archive.  Then double click on the dmg archive to see the installer pkg.

When you double click on the installer pkg to run it and go thru the steps you 
will get to a window showing the install path.  Type in the path 
/Applications/freesurfer in the installer window and then click on Next.

Then when the installer finishes you should have a subdirectory 
/Applications/freesurfer/v93

The new v93 subdirectory needs to look like it has the MCRv84 distribution 
name.  So save the MCRv84 distribution by just moving it aside as 
something with a different name like WAS_MCRv84

$ sudo cd /Applications/freesurfer
$ sudo mv  MCRv84  WAS_MCRv84

Use a soft link to allow the new v93 directory to be accessed with the old 
MCRv84 directory name ...

$ sudo ln  -s  v93 MCRv84

Now when you ls /Applications/freesurfer/MCRv84 you will really see the newer 
R2017b matlab release under the v93 subdirectory.

The Matlab installer will probably say to set the environment variable 
DYLD_LIBRARY_PATH and show paths with /Applications/freesurfer/v93   I 
think that is OK since now there is both the real subdirectory 
/Applications/freesurfer/v93 and also the soft link MCRv84 that points to it.

If you want to put everything back to the way it was then,

$ sudo cd /Applications/freesurfer/7.2.0
$ sudo rm MCRv84
$ sudo mv  WAS_MCRv84  MCRv84

- R.

On Nov 22, 2021, at 00:15, Lab of Autism and Developmental Neuroscience,
Lab of Autism and Developmental Neuroscience  
wrote:External Email - Use 
CautionHello 
Eugenio, Thank you so much for your response. Here is a large section of 
the error message I got while running hippocampal subfields. Please let me know 
if more details are 
needed!  
      Segmentation violation detected at Fri Nov 12 14:26:43 
2021Configuration: 
 Crash Decoding     : Disabled  Current Visual    
 : Quartz  Default Encoding   : ISO-8859-1  MATLAB 
Architecture: maci64  MATLAB Root        : 
/Applications/freesurfer/MCRv84  MATLAB Version     : 
8.4.0.150421 (R2014b)  Operating System   : Darwin 20.6.0 Darwin 
Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; 
root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64  Processor ID    
   : x86 Family 6 Model 85 Stepping 4, GenuineIntel  Software 
OpenGL    : 0  Virtual Machine    : Java 1.7.0_55-b13 
with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode  
Window System      : QuartzFault Count: 1Abnormal 
termination:Segmentation violationRegister State (from fault):  RAX = 
  RBX =   RCX = 
  RDX =   RSP = 
  RBP =   RSI = 
  RDI =    R8 = 
   R9 =   R10 = 
  R11 =   R12 = 
7c6edd00  R13 = 7fff203e54bd  R14 = 
7fff87147d38  R15 = 7c6edda0  RIP = 
3002  RFL = 7f9f5ca7bc80   CS = 
   FS =    GS = 
00010a6d1560Stack Trace (from fault):[  0] 0x00010a320e64 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052[  
1] 0x00010a324a2a 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906[  2] 0x00010a324477 
/Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119[  3] 
0x00010dcd9b7a 
/Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146[  4] 0x00010dcd9e58 
/Applications/