Re: [Freesurfer] Qdec crash while analysis almost finished

[Greve, Douglas N.,Ph.D.]

I'm not sure I understand. Are you using v6 qdec with a 5.3 license file?

On 1/13/2021 2:54 AM, 
chenb...@mail.sysu.edu.cn wrote:

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Hi, dear Freesurfer experts,


I recently came across an invalid Freesurfer license key error while using 
v5.3, and I tried apply for another license key, it just sent me the same 
license key as I have apply before. Then I put the licence file to 
/usr/local/freesurfer and has changed the name to .license as well. But it 
still doesn't work. Owing to the version I used last time was v6.0, so I 
reinstall a v6.0 and use the same license file.

But here comes the new problem, when the analysis almost finished, qdec just 
crash and disappear, parts of the contents in the command window are:

""

Writing results
  lh-Avg-Intercept-thickness
maxvox sig=1e+10  F=3846.45  at  index 14 0 0seed=1611502349
  lh-Diff-PCE-CON-Intercept-thickness
maxvox sig=3.52355  F=15.3058  at  index 11472 0 0seed=1611502349
mri_glmfit done
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to /media/lava/DATA/ESSAY/FirstWave/qdec/Untitled/contrasts.sig.mgh

--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

"""

I wonder what was the question?  Appreciate for any suggestions.



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Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

[Greve, Douglas N.,Ph.D.]

Sorry, I have no idea what could be wrong. Version 5.0 was 10 years ago:). You 
can try copying the v5.3  mri_convert into v5.0, but I suspect that the error 
will crop up in other places. The other thing you can try is to convert the 
file with 5.3 and then see if 5.0 runs on that file

On 1/12/2021 8:54 PM, Dowling, Kevin Francis wrote:
Hi Dr. Greve,

Thanks so much for your reply. I ran the command as instructed (bolded) in 5.0 
(and again in 5.3 for comparison, since that ran fine in my earlier 
troubleshooting efforts) and have placed the terminal outputs below.

In 5.0 the output I received in the terminal:

(nmr-stable5.0-env) mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
$Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30 nicks Exp $
reading from 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii...
Segmentation fault (core dumped)

And in 5.3 this was the result, which seemed to run normally:

(nmr-stable53-env) mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.101076, -0.994877, 0.0017413)
j_ras = (-0.0677184, 0.0051337, -0.997691)
k_ras = (-0.992571, 0.10096, 0.0678903)
writing to deleteme.mgz...

Thank you very much for your help, and for any thoughts you might have.

Kind regards,
Kevin

Date: Tue, 12 Jan 2021 15:45:37 +
From: "Greve, Douglas N.,Ph.D." 
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation Fault During mri_convert
running FS 5.0
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<63bb4542-e9df-d7cc-926b-0731b6009...@mgh.harvard.edu<mailto:63bb4542-e9df-d7cc-926b-0731b6009...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"

For some reason, it is not capturing the terminal output in the log files. Can 
you just run
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
and send me the terminal output?

On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote:
Hello FreeSurfer experts,

We have some old clinical structural data we processed using version 5.0 and 
had extensively edited manually. We?re now hoping to re-process the data in 
version 5 to regenerate copies of the subjects that are free of manual edits. 
So far (because of the below core dump error), I?ve tried doing this two ways, 
first by running recon-all -autorecon-all -clean -s  on copies of our 
manually edited data and, secondly, by using from the original, unaltered 
MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s  
(which fails before we would then run recon-all -autorecon-all -s ). 
In both cases I?ve run into an error I never encountered when last working with 
this data 2 years ago in version 5. Specifically I get a ?Segmentation fault 
(core dumped)? when mri_convert is invoked. I?ve enclosed a copy of the 
recon-all.log and recon-all.error files as attachments and provided the 
specific commands that seem to trigger the core dump below (from 
recon-all.error f
ile). I looked on the mail archive but I wasn?t able to find any answers.

I?m running version 5.0 (as that is the version our manually edited data was 
processed in):
setenv USE_STABLE_5_0_0
source /usr/local/freesurfer/nmr-stable50-env

build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
I?m running Red Hat Enterprise Linux Release 6.7 (Santiago)

The specific commands that appear to be causing the (Segmentation fault) core 
dump in each of the two different cases are below (taken from recon error log):

When running: recon-all -i ./path/to/MEMPRAGE.nii -s  the error occurs 
with..
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz

When running: recon-all -autorecon-all -clean -s  the error occurs 
with..
mri_convert 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz 
--conform

Notably, when I tried running the same commands (bolded above) in version 5.3 
(source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, 
leading me to wonder if this is a software-version interaction issue. (In case 
it has any bearing, I?m running all of this while ssh?d into the Mar

Re: [Freesurfer] matrix is ill-conditioned or badly scaled

[Greve, Douglas N.,Ph.D.]

NaN will not work for this. You can't do incomplete designs with an FSGD. You 
can create your own design matrix and pass it with --X, otherwise you'll have 
to exclude those subjects or put some reasonable (eg, imputed) value

On 1/12/2021 6:35 PM, Julie Ottoy wrote:

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Hi freesurfer experts,

I am trying to run a GLM fit between cortical thickness and some other 
continuous marker. My cortical thickness were stacked before using the 
mris_preproc and surf2surf commands.
I have an FSGD file with the same subjects as used during the stacking of the 
thickness maps, but I added a new continuous regressor (my independent variable 
of interest). However, some subjects have a missing value for this regressor, 
so I added NaN. This makes me run into the following error. When I replace the 
NaN values by random numbers in the FSGD, it all runs fine.

M = [ ...
 1.0  0.99577  0.70711  0.98278  0.97547 -0.97111  nan
 0.99577  1.0  0.70628  0.97775  0.97819 -0.95833  nan
 0.70711  0.70628  1.0  0.68252  0.70488 -0.70032  nan
 0.98278  0.97775  0.68252  1.0  0.95399 -0.96466  nan
 0.97547  0.97819  0.70488  0.95399  1.0 -0.92863  nan
-0.97111 -0.95833 -0.70032 -0.96466 -0.92863  1.0  nan
 nan  nan  nan  nan  nan  nan  nan  ]
Normalized matrix condition is 1e+08
Design matrix --

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.


I made sure that my FSGD file does not have any weird characters, so i applied 
the cat fsgd.txt | sed 's/\r/\n/g' > new.fsgd.txt, but this also didn't help.

Thank you for your help,
Julie





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Re: [Freesurfer] almost empty mask.mgh with glmfit

[Greve, Douglas N.,Ph.D.]

A 0 value usually indicates a bad or uninterpretable voxel which you would not 
want to include in your analysis. You can, of course, by not pruning. But I 
think you need to answer the question as to why the values are 0. Is 0 
interpretable in this case?

On 1/11/2021 6:15 PM, Julie Ottoy wrote:

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Dear Doug,

I was wondering why the flag --prune is recommended (petsurfer website) when 
creating a stacked pet file and during surface-smoothing. If I understood 
correctly, this would set all vertices that are 0 in at least one subject to 0 
("set vox to 0 unless all frames are non-zero")? In my non-pvc data, it seems 
as though a lot of the surface-projected values are 0. Hence, when I perform a 
surface-based regression between PET and a regressor and I use the --prune flag 
during mri_concat, I don't get any results.

Thank you!
best regards
Julie



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Re: [Freesurfer] Non-uniform voxel size

[Greve, Douglas N.,Ph.D.]

I've just created a new version of gtmstats2table (attached). This will take a 
--volume flag to report the volume of the ROIs instead of the uptake


On 1/6/2021 6:00 PM, Julie Ottoy wrote:

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Thank you Doug!
I have another question related to voxel size.

In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels. 
However, is there a way to easily retrieve the volume (instead of NVoxels) for 
each ROI within the gtm.stats file? I know that you should rescale by the pet 
voxel size; however, I have a multi-site study with all different voxel sizes.
Or is there perhaps a way to apply the "aparcstats2table -meas volume" command 
but get the same ROIs outputted as those in the gtm.stats file?

Thank you for the info!
Julie

On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
No, not a problem.


On 12/21/2020 12:52 PM, Julie Ottoy wrote:

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Dear freesurfer team,

I am dealing with PET scans that were acquired at different sites. They do not 
have uniform voxel size and dimensions. I was wondering if this would be an 
issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 
0.5" and vertex-wise PET group-analyses. Should I resample to a uniform 
voxelsize prior to these steps or does freesurfer take care of this issue 
internally?

Thank you for the information.
Best regards
Julie



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#!/bin/tcsh -f
# gtmstats2table - sources
if(-e $FREESURFER_HOME/sources.csh) then
  source $FREESURFER_HOME/sources.csh
endif

set VERSION = '$Id$';

set output = ();
set gtmdirlist = ();
set meas = uptake

set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:

set StartTime = `date`;
set tSecStart = `date '+%s'`;
set year  = `date +%Y`
set month = `date +%m`
set day   = `date +%d`
set hour   = `date +%H`
set min= `date +%M`

set outdir = `dirname $output`
mkdir -p $outdir
pushd $outdir > /dev/null
set outdir = `pwd`;
popd > /dev/null

#
rm -f $output
set stfile = $gtmdirlist[1]/gtm.stats.dat
set roilist = `cat $stfile | awk '{print $3}'`
echo "GTM $roilist" >> $output
@ nth = 0
foreach gtmdir ($gtmdirlist)
  @ nth = $nth + 1
  set stfile = $gtmdir/gtm.stats.dat
  switch($meas)
case "uptake"
  set st = `cat $stfile | awk '{print $7}'`
  breaksw
case "voxels"
  set st = `cat $stfile | awk '{print $5}'`
  breaksw
case "volume"
  set st0 = `cat $stfile | awk '{print $5}'`
  set mask = $gtmdir/aux/mask.nii.gz
  set cmd = (mri_info --voxvol $mask --o /tmp/gtmstats2table.$$.dat)
  echo $cmd 
  $cmd
  if($status) exit 1
  set voxvol = `cat /tmp/gtmstats2table.$$.dat`
  rm -f /tmp/gtmstats2table.$$.dat
  set st = ()
  foreach m ($st0)
set mst = `echo "$m*$voxvol" | bc -l `
set st = ($st $mst)
  end
  breaksw
  e

Re: [Freesurfer] parcellation-based connectome viewing in freeview.

[Greve, Douglas N.,Ph.D.]

this might be something you can do in matlab with the function below (found in 
$FREESURFER_HOME/matlab)


function surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
% surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
%
% Example:
% I have three annotations
%   annotnames = strvcat('superiortemporal','insula','postcentral');
% with matchine values
%   annotvals = [1.1 2.2 3.7];
% I want to create a surface overlay with all the vertices in a
% given annotation having its corresponding value (ie, all vertices
% in superior temporal gyrus being a value of 1.1, etc)
%
% Run these commands in matlab
% annotnames = strvcat('superiortemporal','insula','postcentral');
% annotvals = [1.1 2.2 3.7];
% annotfile = '~/subjects/fsaverage/label/lh.aparc.annot';
% surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile);
% clear mri
% mri.vol = surfoverlay;
% MRIwrite(mri,'vals.mgh');
%
% Run this command from a linux shell:
%   tksurferfv fsaverage lh inflated -aparc -ov vals.mgh -fminmax .01 1
%



On 1/6/2021 10:11 AM, Octavian Lie wrote:

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Dear All,

I have a destrieux-based connectome weight matrix, and wanted to see the edge 
weights between parcels as color-coded activations in freeview, something like 
the attached fig. I think that would be possible, if able to transform the 
weights txt file (symmetric matrix, it could be a .dat file) into an .mgh file 
to overlay it in freeview. Please let me know if it can be done, and how to, or 
there is another way.

Thank you,
Octavian



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Re: [Freesurfer] Editing Recon-all on Different Computers

[Greve, Douglas N.,Ph.D.]

Yes, i think that is still fine

On 1/5/2021 8:18 PM, Boa Sorte Silva, Narlon wrote:

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Hi Allison
As a follow-up to this question

Applying gcut to improve skull stripping when making the manual edits on a 
different computer be a problem (still same FS version for MAC)?

Best regards,
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon

On Dec 9, 2020, at 4:02 PM, Player, Allison A. Stevens 
mailto:allison.stevenspla...@mgh.harvard.edu>>
 wrote:

[CAUTION: Non-UBC Email]
Hi Nárlon Cássio,
Editing on different computers is fine as long as you’re processing them on the 
same machine, as you indicated.
Allison

On Dec 9, 2020, at 6:54 PM, Boa Sorte Silva, Narlon 
mailto:narlon.si...@ubc.ca>> wrote:


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Hi FreeSurfer community,

Are there any reservations for editing recon-all outputs (cross, base, or long) 
on a different computer from which the images were originally processed? Both 
computers are Mac and have the same FreeSurfer version (7.1.1).

I intend to use the same computer when re-running the edited images in in 
recon-all pipeline, but wanted to know whether editing on a different computer 
would be an issue.

Thank you,
Best regards

Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon

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Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

[Greve, Douglas N.,Ph.D.]

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD 
files as found in  $FREESURFER_HOME/average/mult-comp-cor

On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:

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Dear Freesurfer Experts,

I’ve all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It’s quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
 --csd 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
 --csdpdf 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat
 --vwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh
 --vwsigmax 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat
 --oannot 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot
 --bonferroni 2 --surf white
Merging CSD files
ERROR: could not open 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version 7.1.0
hemi   = lh
srcid  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 MGH
ocnid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 MGH
sumfile  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
subjectsdir= /home/xiaoxu/8YearOldNiiB1
FixMNI = 0
Found 148772 vertices in mask
Found 148772 vertices in mask
Found 148772 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm
1.0   0.0   0.0   0.0;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.0;
0.0   0.0   0.0   1.0;

Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot
mri_surfcluster supposed to be reproducible but seed not set
reading colortable from annotation 

Re: [Freesurfer] Desikan Killiany Atlas Node Coordinates

[Greve, Douglas N.,Ph.D.]

If you want the coordinates, you can also run mri_segcentroids on the 
aparc+aseg.mgz in fsaverage. Or, if you want them in mni152 space, you can run 
the 152 through recon-all and then run mri_segcentroids on the resulting 
aparc+aseg.mgz

On 1/5/2021 11:01 AM, Mora, Jocelyn S. wrote:
Hi Jessica,

FreeSurfer reports "Talairach MNI" coordinates which are MNI305 space. It may 
be helpful to take a look at our site which details FreeSurfer coordinate 
systems 
here.

I also wonder if what you are looking for can be answered by 
this 
past mailing list thread. Hope these notes help.

Cheers,
Jocelyn

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

 on behalf of Hua, Jessica 
Sent: Monday, January 4, 2021 6:43 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: [Freesurfer] Desikan Killiany Atlas Node Coordinates


External Email - Use Caution

Dear FreeSurfer,

I would like to conduct a network based statistical analysis. One of the inputs 
in the NBS toolbox is to provide a list of MNI coordinates for each of the 
brain regions in the parcellation. Is there an established list of MNI 
coordinates for the Desikan-Killiany atlas? And if not, do you know how I could 
identify the center MNI coordinate for each of the brain regions in this atlas?

Best,

Jessica



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Re: [Freesurfer] eTIV=0.0 on volumes where control points have been added manually

[Greve, Douglas N.,Ph.D.]

Hi Julia, this is a bug. We've fixed it in our development version, but for you 
there are a few option. One is that you can just get the value from aseg.stats 
(asegstats2table). Or you can run recon-all with these flags -talairach 
-parcstats -parcstats2 -parcstats3

On 12/29/2020 7:34 AM, Julia Lam wrote:

External Email - Use Caution

Dear all,

I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running 
aparcstats2table on volumes where I've added control points. However, when 
aseg2stats was used, the variable EstimatedTotalIntraCranialVol was different 
from 0 on all, including the edited ones. Why is that?

I've attached the logfile from one of the subjects where I used control points.

I really appreciate any help you can provide.

Yours sincerely
Julia Lam






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Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 36 Topic 14. Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory (Greve, Douglas N., Ph.D.)

[Greve, Douglas N.,Ph.D.]

Sorry, I lost track of the original thread. Can you explain it or say why you 
are not running recon-all?

On 1/4/2021 9:27 AM, Camerino, I.L. (Ileana) wrote:

External Email - Use Caution
Dear Douglas,

Thank you so much for your reply.

After trying: mri_em_register -mask brain.mgz -p .5 nu.mgz 
$FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
I got the following error:  using MR volume brain.mgz to mask input volume...
using top 50.0% wm points as control points

== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/opt/freesurfer/6.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/brain.mgz, 
-1): could not open file
mri_em_register: could not open mask volume brain.mgz.

In fact the the file brain.mgz is not present in the mri folder.

I am a bit lost since I am getting a different error every time I try to solve 
the previous one and I do not understand what is the problem exactly.

The first error I got after running recon all on this subject (with a massive 
stroke on the left hemisphere) is a watershed error. So I added the control 
points and run:  recon-all -autorecon2-cp -autorecon3 -subjid 
/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056. After which I got the 
error:

mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/norm.mgz, 
-1): could not open file
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
mri_normalize: could not open source file norm.mgz

Finally to solve the above error I run: mri_em_register -mask brain.mgz -p .5 
nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.lta but I got yet a new error: -1): could not open file 
mri_em_register: could not open mask volume brain.mgz.

Please could you let me know how can I understand what is the problem and how 
can I solve it?

Best regards
Ileana Camerino

PhD candidate
Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618







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Re: [Freesurfer] recon-all -hires option

[Greve, Douglas N.,Ph.D.]

If you want to try to do it systematically, you can add -wsless (should reduce 
the agressiveness of the skull strip)

On 1/4/2021 3:52 AM, 
falk.luesebr...@med.ovgu.de wrote:

External Email - Use Caution

Hi Simon,


in case your surfaces (and other outputs) look fine, there is no need to worry 
about the skull stripping too much. However, in case you what to do something 
about this you can do either of the following.


Which version are you using? I assume v6? In v7 the hires option basically has 
changed to what was known as the HCP pipeline before. Here, only the surface 
related parts of FreeSurfer are handled in native space. The other stages are 
handled in resampled 1mm space. Therefore, you will benefit from your higher 
resolution, while not having any of these issues. There are also some other 
stages included which may help with high resolution 3T data (e.g. denoising 
prior to surface placement).


In case you want to stick with v6 and what to run everything in native space, 
you can get better skull stripping following the first few steps from this 
guide I put together few years ago (and is still valid today):

https://secure-web.cisco.com/1cP9GZTFwQIDCR-WcWJPQA-tzd6FKvDGnFtvVRx4GcsgT8p3OTg1qClc-Hq--pwQhCCzMU0__8jGrDJugvajjUrRsHuOiOAOaxFIABpq99gkP60a9dQB2KDoTXXK3jmPU66oLOS0VCPGhxL5_1DVsdUVWefugGXKw6nA29BxCzBaKOfrZBOuL4bxxOBVIVUa1E3EfYzL7gMPd6g5Xvqz1zUtRdv-sQtDWX98QT7ZaoRAjjeDZvgWcqjhe9WNHXE5kInE_ok7pb2gunRxE78zPKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHiResRecon


What you basically do is to run the 1mm stream to create a nice brainmask (or 
any other tool you like), resample that to the resolution of your high 
resolution stream and apply the mask after the normalization stage. Then 
continue with autorecon2 and autrecon3.


Best,

Falk



Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von S.R. Poortman 

Gesendet: Montag, 4. Januar 2021 09:13:11
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Fw: recon-all -hires option


External Email - Use Caution

Dear list members,

As a PhD student working on longitudinal child and adolescent T1-weighted data 
(.75x.75x.8 mm3) acquired at 3T (age range: 8 - 18 at baseline; 11 - 24 at 
follow-up), with the aim of doing cortical laminar analyses eventually, I am 
interested in getting the most of our lab's submillimeter resolution data. 
Therefore, in addition to a default recon-all run (with the -3T option 
enabled), I ran a separate recon-all with both the -3T and the -hires option 
enabled (with mris_inflate -n 50 added to the expert file), resulting in the 
following two runs:
recon-all -all -i ${subj} -subjid ${SUB_ID} -3T
and
recon-all -all -i ${subj} -subjid ${SUB_ID}  -3T -hires -expert $EXPERT_FILE
Now, the surfaces (i.e., lh.pial, lh.white, rh.pial, rh.white) seem to be 
calculated more accurately for most brain regions, indeed, which looks very 
promising. However, the brainmask.mgz turns out to be of poor quality for a 
number of our subjects, cutting away a substantial portion of the brain. See 
the image below for an example of the same subject, on which both runs have 
been performed. The same slices are shown for each run. As can be seen in the 
image, a part of the the temporal region of the brain has been excluded in the 
brainmask.mgz of the -hires run (left in the image).

[cid:b4d26f40-11bb-4d8f-888c-ab4da9fea062]

Is there anything I can do, such as adjusting certain parameters, to prevent 
this from occurring? It would be a shame if I couldn't make use of the -hires 
option due to this, as it does seem to be a promising option in all other 
aspects.

Thank you for considering my question. I look forward to hearing from you.

Good holidays to you!

Kind regards,
Simon Poortman (Erasmus MC, Rotterdam, the Netherlands)





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Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

[Greve, Douglas N.,Ph.D.]

For some reason, it is not capturing the terminal output in the log files. Can 
you just run
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
and send me the terminal output?

On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote:
Hello FreeSurfer experts,

We have some old clinical structural data we processed using version 5.0 and 
had extensively edited manually. We’re now hoping to re-process the data in 
version 5 to regenerate copies of the subjects that are free of manual edits. 
So far (because of the below core dump error), I’ve tried doing this two ways, 
first by running recon-all -autorecon-all -clean -s  on copies of our 
manually edited data and, secondly, by using from the original, unaltered 
MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s  
(which fails before we would then run recon-all -autorecon-all -s ). 
In both cases I’ve run into an error I never encountered when last working with 
this data 2 years ago in version 5. Specifically I get a “Segmentation fault 
(core dumped)” when mri_convert is invoked. I’ve enclosed a copy of the 
recon-all.log and recon-all.error files as attachments and provided the 
specific commands that seem to trigger the core dump below (from 
recon-all.error file). I looked on the mail archive but I wasn’t able to find 
any answers.

I’m running version 5.0 (as that is the version our manually edited data was 
processed in):
setenv USE_STABLE_5_0_0
source /usr/local/freesurfer/nmr-stable50-env

build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
I’m running Red Hat Enterprise Linux Release 6.7 (Santiago)

The specific commands that appear to be causing the (Segmentation fault) core 
dump in each of the two different cases are below (taken from recon error log):

When running: recon-all -i ./path/to/MEMPRAGE.nii -s  the error occurs 
with..
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz

When running: recon-all -autorecon-all -clean -s  the error occurs 
with..
mri_convert 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz 
--conform

Notably, when I tried running the same commands (bolded above) in version 5.3 
(source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, 
leading me to wonder if this is a software-version interaction issue. (In case 
it has any bearing, I’m running all of this while ssh’d into the Martinos 
servers.)

I suspect I may have missed something very simple, but I would be very grateful 
for any suggestions for how I might try to overcome this issue. I’m happy to 
provide clarification or any additional information that may be helpful.

Thank you,
Kevin

Kevin F. Dowling
Per-Diem Clinical Research Coordinator
Brain Genomics Laboratory
Department of Psychiatry
Massachusetts General Hospital
MD/PhD Candidate
University of Pittsburgh &
Carnegie Mellon University MSTP



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Re: [Freesurfer] The lookuptable value of Virchow–Robin space

[Greve, Douglas N.,Ph.D.]

Probably
77  WM-hypointensities  200 70  255 0


On 1/2/2021 1:11 PM, Aaron Tanenbaum wrote:

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Ideally, what should Virchow–Robin space be labeled as.



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Re: [Freesurfer] Transform rescaled non-pvc PET to surface

[Greve, Douglas N.,Ph.D.]

If you've run mri_gtmpvc already, you can add --save-input and it will save a 
file called input.rescaled.nii.gz which will be rescaled to your reference 
region

On 12/29/2020 4:19 PM, Julie Ottoy wrote:

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Dear Freesurfer team,

I have a question related to petsurfer. On the website, it is stated that "If 
you are not using PVC, you can use the template.reg.lta to sample the PET 
volume onto the surface using mri_vol2surf, then apply standard surface-based 
analysis."

However, I was wondering how to do this for PET data that I first want to 
normalize to a reference region (to perform group-wise glm analyses 
afterwards). For example, I want to transform the "non-pvc and pons-rescaled 
PET volume" to the surface. Is there a way to easily do this? Or should I use 
the --scale flag with vol2surf and input the non-pvc reference region value for 
each subject reading from the gtm.stats.dat file, which I got from the 
mri_gtmpvc with --psf 0 --no-tfe --no-rescale?

Thank you for the help!
Best regards
Julie




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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Greve, Douglas N.,Ph.D.]

Try using --replace 29 2


On 12/29/2020 12:48 PM, Julie Ottoy wrote:

External Email - Use Caution

Hi Doug

Thanks for your reply. I tried both your suggestions, but it seems as though 
they both ran into an error.

For your first suggestion, i.e. adding --replace 29 3 to the command line of 
gtmpvc, I get the error:

Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz

Loading seg ctab 057_S_5295re/mri/gtmseg.ctab

Reading 057_S_5295re/mri/gtmseg.lta

Replacing 19

Pruning ctab

ERROR: CTABpruneCTab(): ctab does not have segid 3


For your second suggestion, i.e. I replaced the following line in the ctab:

  29  Left-undetermined   135 206 2350  -1

==> replaced by:  29  Left-undetermined   135 206 2350  3


I get the error:

Computing Seg in input space

Building GTM DoVoxFracCor=0

ERROR: creating region for nthseg=12, segid=29, Left-undetermined

It may be that there are no voxels for this seg when mapped into the input 
space.

Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the 
registration

 Build time 5.9690, err = 1


Thank you,

Julie

On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can use the fix from my previous email or you can add the following line 
any were into the gtmseg.ctab file:
 29  Left-undetermined   135 206 235 0 3


On 12/18/2020 11:06 PM, Julie Ottoy wrote:

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Sorry I would like to correct my previous post. The subject also failed with 
PVC.
I see now that the issue is happening during the gtm seg stage where it gives 
the error: WARNING: segid   29 Left-undetermined tissue type is not set.
For your information: I ran the standard FS and petsurfer pipeline as outlined 
on the wiki. I tried two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm --subseg-cblum-wm

Thank you for your help,
Julie

On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:

External Email - Use Caution

Dear Doug,

I have the same issue as the people below. I was wondering if this was solved 
in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got 
the following error in only one of my subjects. When I ran the same subject 
with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz 
--default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o 
/gtmnopvc.output.ceregrey --rescale 8 47
sysname  Linux
hostname -
machine  -
user -
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Any suggestions would be appreciated!
Thank you,
Julie

Re: [Freesurfer] mri_gtmpvc error: failed tissue type 
check<https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGDCYbw1nr7Bymh0JNbA3Nr4M_m3-TZzftvlgMiJh7YiC6aUDW4Al3Wj4Kuy-05sd4QjU4E_RzWvbOfb_BTd5VaY6BPCSTWz6zWkEU0xuqeLNwwPRnm1yANvQkKZrMAWw2Gw7xnEbbIx95EqXWVkcRYx-x2scLfRIy4vfC9Cwn0nm4LrwA7h_KSoSDmXwnNLtLoWCfmI3LlkSE6EtVO2bwfNHaGn2-d6rSu0cljwjoiw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55983.html>
2017-11-25<https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8hnIkonyOL9FxrLNrp4Bj2WuN0PTQlUGm_PJQva6MLutv6BMWs-SO763W-gwW1nAT6N4vj217JzAEoSXtBbWL5JUyfL-O7BWGLfrj_ULjoLxBYnq2LcSNQgj9kva8w0E0bdnIFYTLoXYkJqjYbk7i-67h2LWjuOMCsdK3wV31zmywpixGXpXL85YXKxMmEETIQFPv9cZG3dAO4WLNFtjdVE1ZXCWD0o5zbpJqBYb5A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20171125%26o%3Dnewest%26f%3D1>
 
Thread<https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1>
 Douglas 
Greve<https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F

Re: [Freesurfer] Group Analysis Question

[Greve, Douglas N.,Ph.D.]

I think that contrast computes Female-Male regressing out Dx and age. If you 
want HC vs MS, then use
-0.5 -0.5 0.5 0.5


On 12/29/2020 4:52 PM, Swanson,Clayton wrote:

External Email - Use Caution

Hi Freesurfer Team,
I am performing an analysis on 23 HC and 26 people with MS and I would like to 
perform the stats appropriately. I would like to control for (or regress out) 
age and sex.  Therefore, I created my FSGD file which has 4 classes (HC_Male, 
HC_Female, MS_Male, MS_Female) with age being the only variable.  My contrast 
for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a 
permutation analysis, so I set it up like this:

#!/bin/tcsh
setenv study $argv[1]
foreach meas (thickness volume)
  foreach hemi (lh rh)
foreach smoothness (10)
  foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
mri_glmfit-sim \
  --glmdir {$dir} \
  --perm 1000 1.3 pos \
  --cwp 0.05  \
  --2spaces \
--overwrite
  end
end
  end
end

After running the permutation, my next steps were to view the results in 
Freeview with the command [ freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh 
] because it’s my understanding that would overlay the cluster-wise corrected 
map and the view I get is an entirely yellow hemisphere. However, there are no 
significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I 
am a bit confused. Also, when I look at the uncorrected results with the 
sig.mgh file there are a number of spots on the hemisphere.

Does this result mean that there are no cortical thickness differences between 
HC and MS when controlling for Age and Sex?  Or does this result mean something 
different?  What could be the next analysis steps I could perform?

My goals are to assess cortical thickness differences between HC and MS.

Thanks for any help you can provide,

Clayton

Clayton Swanson MS
Graduate Research Assistant & PhD Candidate
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu
(He/Him)




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Re: [Freesurfer] talairach.lta coordinate spaces

[Greve, Douglas N.,Ph.D.]

Note that FS will "conform" the volume to be coronal with axes aligned 
with the major scanner axes, so that will undo a lot/all of your rotation

On 12/29/2020 11:37 AM, Fischl, Bruce wrote:
> p.s. oh, and the .lta format is ascii so you can just look at it to see if it 
> is vox2vox or ras2ras
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Tisdall, Dylan
> Sent: Thursday, December 24, 2020 11:41 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] talairach.lta coordinate spaces
>
>  External Email - Use Caution
>
> Hi list,
>
> I'm trying to understand whether the talairach.lta transform is from the 
> image-axes RAS to talairach or the scanner-axes RAS to talairach. Basically, 
> if I rotate the imaging FOV and scan the same subject, should I expect that 
> to change talairach.lta or not? My confusion stems from the discrepancy 
> between what the scanner terms RAS coordinates (aligned to the gradient axes) 
> vs. what might be plausibly called RAS in the image coordinates (aligned to 
> the FOV axes).
>
> The underlying goal here is to try to evaluate how gradient-axis-aligned 
> someone's head was when they were loaded in the scanner.
>
>
> Thanks,
> Dylan
>
> ---
> Dylan Tisdall, PhD
> Research Assistant Professor
> Department of Radiology
> Perelman School of Medicine
> University of Pennsylvania
>
> Room D406 Richards Medical Labs
> 3700 Hamilton Walk
> Philadelphia, PA 19104
>
>
>
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Re: [Freesurfer] error in running tkregisterfv (Greve, Douglas N., Ph.D.)

[Greve, Douglas N.,Ph.D.]

Sorry, I deleted the previous emails. Can you repost with our previous 
exchanges so I know the context?

On 12/28/2020 9:30 AM, Peter de Best wrote:

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Dear Dr. Greve,

Thank you so much for the information. However, after adjusting the 
registration file to *.lta, I get the same error message. It will probably help 
me correctly coregister func & anat in the future, but the issue seems more 
likely to be connected to some setting that I cannot seem to find...

Do you have any suggestions/ tips?

Best regards (and happy new year),

Peter



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Re: [Freesurfer] Access to datasets used for validation of sbTIV and eTIV measures

[Greve, Douglas N.,Ph.D.]

ADNI30 is lost by now. For SASHA, we don't have the actual manual 
labels, but we still have the TIV generated from those labels. I'm 
pretty sure that we cannot release that data. Sorry, not much luck here

On 12/26/2020 2:49 PM, Erus, Guray wrote:
>  External Email - Use Caution
>
> Hello FreeSurfer Developers,
> I'm working on the validation of a method that calculates ICV. The wiki pages 
> on eTIV and sbTIV:
> 
> https://secure-web.cisco.com/1NfwRceKeD3VTf9pMcEK-JbxIvMnSdQdPlMoLFc8Asj7-1mBFiTJlMNaoEFPBhE649Q0sHw6nC5KDfCvm_3APiG0GtKRV7O-UbZ-EsvmRZ0dcZk4kaqqsAfwfeAeVfJW7EpcGj6BrZMsg_QKjTvr4Gzdnc1WqmMkisncDI-ZaxVbTlr-Cq_pBJUu9mer5_4Kq-5N5o8o_oTwN8NpkpYY-M5DAbh4o2AqvgX186CBDe1chFBKKnPNC1T4WZtrb7I6pTz9dYbLRGxPqtiDHXgvw2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FsbTIV
> 
> https://secure-web.cisco.com/1NnGHZWJ6QIknzbA50Q86PSKxQrceCNCSBmR1j4U6EVMlcHWfhwaTDF2CXiZUc2yTKpEjR7VjQb_zasUea3Py-YGQ3SGUHiyZ4xcu6R_yz5Bag9LLLFXjIOUD8ciMMVS-YOi6seNRmzf_ZR-Q41jMBwfCxoDIQzneBxckctWYAsmjq6N5tzDaH7cKFxzP6TBpUTAprLdANCFBnPH4vsuC1i1u2CYTXY2E9bAHfM1QtszG-xb2q9ztMYP0ALUpAvm6fEvEgZm6ZY05DWXrEXkjvg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV
> include very useful information related to my work. These pages refer to 2 
> datasets (SASHA and ADNI30) with manual ICV masks. The text also indicates  a 
> path for one of these datasets:
>   "... These subjects are found in /space/freesurfer/subjects/atlases/SASHA 
> ..."
> If I understand correctly, this is a local/restricted path that is not 
> publicly available. Is that correct?
> Is there a way I can get access to these datasets for my validation 
> experiments?
>
> Thank you and happy new year!
> Guray
>
>
> Guray Erus, PhD
>
> Senior Research Investigator
> Center for Biomedical Image Computing and Analytics (CBICA)
> University of Pennsylvania
> Richards Building
> 3700 Hamilton Walk, 7th Floor
> Philadelphia, PA 19104
>
>
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Re: [Freesurfer] segmentation fault

[Greve, Douglas N.,Ph.D.]

Please send the recon-all.log file

On 12/25/2020 8:42 PM, Wei Koo wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to run recon2 for a number of subjects, but one of my subjects I 
get the following error when I run the mri_tesellate command:

Removing intersections
Segmentation fault

FreeSurfer version: freesurfer-darwin-macOS-7.1.1.




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Re: [Freesurfer] Question about a feature introduced in FS 7.0 {Disarmed}

[Greve, Douglas N.,Ph.D.]

so, does that mean it is working?

On 12/24/2020 12:19 PM, Aaron Tanenbaum wrote:

External Email - Use Caution

Thank you for responding. So before you responded, I tried a few things out. 
one of them was to make the edit to the image and then run recon-all with 
"-autorecon2-noaseg -autorecon3". I found this to move the surface however the 
aparc+aseg file had the voxel I altered as 247. Last night I tried what you 
suggest with the same alterations to the aseg.presurf file, I found the surface 
and aparc+aseg was unchanged.

On Wed, Dec 23, 2020 at 12:28 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
I don't have any example, but the idea is pretty simple. If you want to freeze 
a point on the surface, open aseg.presurf.mgz and the surfaces for your 
subject, eg,
tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs
Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to 
value 247 (FreezeSurface in  $FREESURFER_HOME/FreeSurferColorLUT.txt)
Then run recon-all with -autorecon2-surfonly -autorecon3


On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:

External Email - Use Caution

So I never got a response for my question. At least can someone tell me the 
recon-all flags needed after editing the aseg.presurf.mgz file.  I am also 
assuming that this feature is also available for 7.1.1.

On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:
I am curious about a feature introduced in FS 7.0  In the release notes it 
says, "Ability to freeze the surface at points labeled 247 in the 
aseg.presurf.mgz" I was interested to know what this feature can do. Do you 
have any examples of when this should be used?

Aaron Tanenbaum



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Re: [Freesurfer] Question about a feature introduced in FS 7.0

[Greve, Douglas N.,Ph.D.]

I don't have any example, but the idea is pretty simple. If you want to freeze 
a point on the surface, open aseg.presurf.mgz and the surfaces for your 
subject, eg,
tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs
Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to 
value 247 (FreezeSurface in  $FREESURFER_HOME/FreeSurferColorLUT.txt)
Then run recon-all with -autorecon2-surfonly -autorecon3


On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:

External Email - Use Caution

So I never got a response for my question. At least can someone tell me the 
recon-all flags needed after editing the aseg.presurf.mgz file.  I am also 
assuming that this feature is also available for 7.1.1.

On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:
I am curious about a feature introduced in FS 7.0  In the release notes it 
says, "Ability to freeze the surface at points labeled 247 in the 
aseg.presurf.mgz" I was interested to know what this feature can do. Do you 
have any examples of when this should be used?

Aaron Tanenbaum



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Re: [Freesurfer] Error

[Greve, Douglas N.,Ph.D.]

Source 7.1.1
Go into $SUBJECTS_DIR
rm fsaverage
ln -s $FREESURFER/subjects/fsaverage
that should do it

On 12/22/2020 8:47 AM, Weerasekera, Akila wrote:
Hello,

I sent a few jobs to launchpad (FreeSurfer segmentation) and they exited with 
an exit=1, this is the error:

"ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! The 
fsaverage link probably points to an older freesurfer version"

I switched from Fs 6 to FS 7.1.1, how do I change the fsaverage link?

Any help is appreciated.
Thank you





Akila Weerasekera, PhD | Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory |

Ratai Lab for Clinical Spectroscopy |


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | 
Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | 
Charlestown, MA 02129


Mobile: (781) 820 4501

aweerasek...@mgh.harvard.edu 

www.nmr.mgh.harvard.edu

https://scholar.harvard.edu/loggia






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Re: [Freesurfer] recon labels.DKT31.manual.nii.gz appears ERROR: Talairach failed

[Greve, Douglas N.,Ph.D.]

Can you send the recon-all.log file?

On 12/22/2020 7:23 AM, 1248742467 wrote:

External Email - Use Caution

Hello, everyone
I have download the labels.DKT31.manual.nii.gz in mindboggle datsets, I want to 
use recon-all command to get lh.labels.DKT31.manual.annot. But, when I run: 
recon-all -i labels.DKT31.manual.nii.gz -s bert5 -all, appears ERROR: Talairach 
failed

--
SUBJECT bert5
DATE Tue Dec 22 19:49:07 CST 2020
USER tj
HOST bme01
PROCESSOR x86_64
OS Linux
Linux bme01 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/home/tj/application/freesurfer/bin/recon-all
PWD /home/tj/application/freesurfer/subjects/bert5/mri
CMD talairach_afd -T 0.005 -xfm transforms/talairach.xfm



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Re: [Freesurfer] Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory

[Greve, Douglas N.,Ph.D.]

Try using RB_all_2016-05-10.vc700.gca instead

On 12/22/2020 5:54 AM, Camerino, I.L. (Ileana) wrote:
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Re: [Freesurfer] No extracerebral CSF in sGTM

[Greve, Douglas N.,Ph.D.]

yes, it does, assuming the segmenation of extra cerebreal CSF is adequate

On 12/22/2020 12:57 AM, Julie Ottoy wrote:

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Dear Petsurfer team

Does the sGTM PVC correct for the uptake in extra cerebral CSF?
If not, how would this affect the reliability of the cortical PVC measures, 
considering the spill-out of grey matter uptake to csf is being ignored?

Thank you!
Best regards
Julie




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Re: [Freesurfer] cluster size and FWER rough equivalence?

[Greve, Douglas N.,Ph.D.]

On 12/21/2020 8:45 PM, Kayle Sawyer wrote:

External Email - Use Caution

We are working on a manuscript revision for an fMRI project that was analyzed 
with FS-FAST 5.3 years ago. We used mri_glmfit, and then we ran mri_surfcluster 
(instead of mri_glmfit-sim) with a vertex-wise threshold of p<0.001 and a 
cluster threshold of 100mm^2. We had applied 8 mm smoothing at the group-level, 
and the voxel size was 3.125x3.125x5 (resampled to fsaverage surface and to 
MNI305).


1. One reviewer asked us to provide a rough estimate of the family-wise error 
rate (FWER) that a cluster threshold of 100mm^2 is equivalent to, or 
alternatively, to re-analyze everything with mri_glmfit-sim permutation. It 
would be simpler to provide the FWER estimate. To get the FWER estimate, we 
referred to Woo et al (2014). However, their simulations were for volume 
analyses, not surface analyses. What is the FWER (roughly) for a primary 
threshold of p<0.001 and cluster threshold of 100mm^2? (Obviously, we are 
hoping for a number less than 0.05.)

Why not run mri_glmfit-sim and just see what the p-value is for that cluster?


2. For the volume, we used mri_surfcluster with a primary (voxel-wise) 
threshold of 0.001 and a size threshold of 300mm^3. If I’m understanding 
correctly, Figure 2 from Woo et al. (2014) suggests a FWER p<0.05 might roughly 
correspond to a cluster size threshold of 200 to 985 voxels (1600 to 7880 
mm^3), depending on intrinsic smoothness. That would likely put our threshold 
of 300mm^3 well above p<0.05. Is this correct?

Again, you can just run mri_glmfit-sim. I would use the version 7 for this one 
though as I think the volume-based GRF might have changed since 5.3. You can do 
the same for the surface-based above, but I think the 5.3 version should be ok


Thanks,

-Kayle




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Re: [Freesurfer] Talairach Failure in recon-subject {Disarmed}

[Greve, Douglas N.,Ph.D.]

That is just the failure detection. Sometimes it generates a false positive. 
Did you check the transform? If the rest of the downstream processes (eg, aseg 
and surfaces) are ok, then you don't need to worrry

On 12/21/2020 6:53 PM, Wei Shao wrote:

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Hi, Freesurfer team

I have met a Talairach Failure problem when running the recon -all for a 
subject, here is the feedback: I tried -notal-check flag, but it might cause 
another problem when I use segmentHA_T2.sh to do hippocampus subfield 
segmentation. So, Could you help me to solve this problem? Thanks.

#
#@# Talairach Failure Detection Mon Dec 21 17:59:09 EST 2020
/scratch/weishao/20191017_BAY10224/sub-BAY10224_Negar/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0., pval=0. < threshold=0.0050)
@#@FSTIME  2020:12:21:17:59:09 talairach_afd N 4 e 0.07 S 0.01 U 0.00 P 18% M 
6672 F 0 R 2777 W 0 c 2 w 65 I 1504 O 0 L 12.75 18.35 27.51
@#@FSLOADPOST 2020:12:21:17:59:09 talairach_afd N 4 12.75 18.35 27.51

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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ERROR: Talairach failed!

Linux gra824 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 
x86_64 GNU/Linux

recon-all -s sub-BAY10224_Negar exited with ERRORS at Mon Dec 21 17:59:09 EST 
2020

Best,
Wei

:



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Re: [Freesurfer] Vertex-wise functional ROI extraction

[Greve, Douglas N.,Ph.D.]

We don't have anything that creates a text file of the time course in 
each voxel, if that is what you mean. In principle you can do it in 
matlab...

On 12/21/2020 4:28 PM, Sussman, Lauren wrote:
>  External Email - Use Caution
>
> Hello!
>
> I would like to extract functional data from a manually created label ROI on 
> the surface on a vertex-wise basis. Funcroi-table-sess appears to only 
> provide averaged values and I would like the value per vertex inside the ROI 
> for the given contrasts. Is there a way to grab this data using Freesurfer?
>
> Thank you!
> Lauren
>
> ___
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Re: [Freesurfer] Non-uniform voxel size

[Greve, Douglas N.,Ph.D.]

No, not a problem.


On 12/21/2020 12:52 PM, Julie Ottoy wrote:

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Dear freesurfer team,

I am dealing with PET scans that were acquired at different sites. They do not 
have uniform voxel size and dimensions. I was wondering if this would be an 
issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 
0.5" and vertex-wise PET group-analyses. Should I resample to a uniform 
voxelsize prior to these steps or does freesurfer take care of this issue 
internally?

Thank you for the information.
Best regards
Julie



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Re: [Freesurfer] PFC segmentation

[Greve, Douglas N.,Ph.D.]

Do you want a binary map? If so, you can run
mri_binarize --i aparc+aseg.mgz --o pfc.mgz --match Id1 Id2 ...
where Id1 ... is a list of segments you want in your binary map as found in 
$FREESURFER/FreeSurferColorLUT.txt, eg, 1028 is left superior frontal

1028ctx-lh-superiorfrontal  20  220 160 0




On 12/21/2020 12:52 PM, Kothapalli, Satya wrote:
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Re: [Freesurfer] monkey atlas D99 {Disarmed}

[Greve, Douglas N.,Ph.D.]

The argument to the --label flag should be a freesurfer label file, this is a 
text file not an nii.gz file.

On 12/21/2020 10:52 AM, Francesca Strappini wrote:

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Thank you!
I run mri_label2vol but I got this error.

mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp 
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
 --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject 
MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
Number of labels: 1
D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Annot File:  (null)
Template Volume: 
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
Registration File: registerNMT2toCassis.dat
Fill Threshold: 0.3
Label Vox Vol:  1
ProjType:   frac
ProjTypeId: 2
ProjStart:  0
ProjStop:   1
ProjDelta:  0.1
Subject:  MonkeyCassis
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: 
-0.49612  -0.0  -0.0   32.0;
-0.0  -0.0  -0.49612   32.0;
-0.0   0.5  -0.0   10.0;
-0.0  -0.0  -0.0   1.0;
Template Voxel Volume: 8.12549
nHits Thresh: 2.43765
Loading registration from registerNMT2toCassis.dat
RegMat: 
-0.99904  -0.03839   0.02093  -1.00375;
 0.02331  -0.06274   0.99776  -29.26276;
 0.03699  -0.99729  -0.06358  -8.60775;
 0.0   0.0   0.0   1.0;
Label RAS-to-Vox: 
 0.49565   0.01905  -0.01038   32.49799;
-0.01835   0.49478   0.03154   36.27051;
 0.01166  -0.03137   0.49888  -4.63138;
 0.0   0.0   0.0   1.0;
  INFO: loading surface  
/usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white
nvertices = 16975
Reading thickness /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (81920) voxels
Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz

�7��ա<�d�TGr��L�� �s�L�f�T�ot�9eOԲ:|��L��� ���s/ ��,�' 
��,3~�铜��s�`�:�ǙG�] �I�Gu ��`�:�[g��>� <�\�٧S 
�N��L���<>�t��Mw��l���n�љ���ǢS �WM�K�4 f��Nu
 W3FfN�TGqt� �Nu �Nf6�V�}�VG�?̄ޭ��x� �[ ꝣy�Ou��/� 
e:%�N�YܺՁ>�e�uu���3�k�:�'O�:���w�[�%��v�Ou�w�ث�t� �^uL��pg 
�^2��ܱ��=�u���8wo�C}�[ {���M&� =<G[�X�3]�㜙췪�|��tI掝�L�� 
w2g�Vu�;�\��(_Og_gN���P�'O3'�Vu�_M���, �̪ѯ�t�I8��q�z��ߓONꗙ �_ �u 
�y�Wu��v�iݯ��x���d��a�'s�03���C��� �=ȣ�xϲ�� ��d5�;���Nf<Ձ���3

  
�s��9� �A�d��A��e��A/�;:���Lr0�y��<��d�s�QѪ���^�Oû]��
mri_label2vol: could not scan # of lines from label file
ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz

Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
Use mri_label2vol to map the segmentation into the fMRI space, then use 
mri_segstats using the --avgwf option to get time courses. Run it with --help 
to get examples

On 11/26/2020 9:16 AM, Francesca Strappini wrote:

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Dear FreeSurfer experts,

I'm trying to use the monkey atlas D99. First, I registered the segmentation 
atlas to the monkey anatomy through bbregister. Now, I need to resample the 
segmentation to the functional data and extract the mean value from each 
functional run using the ROIs contained in the segmentation as masks. I suppose 
I should mri_segstats but I'm not sure how. Any suggestion?

Thank you
Francesca


--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: 
francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>



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Re: [Freesurfer] Anterior insula thickness

[Greve, Douglas N.,Ph.D.]

We don't have an anterior insula segmentation. One thin you can try is to 
divide the insula label with mris_divide_parcellation. If one of those 
subdivisions works for you then you can compute the thickness inside it. You 
might want to do it on fsaverage and then map it back to the individual 
subjects. Or you can just draw the label you want on fsaverage and map it back 
to the individual subjects

On 12/21/2020 9:34 AM, Hanne Van Der Heijden wrote:

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Dear freesurfer experts,

I have a question regarding analysis of cortical thickness.
In the stats folder of each subject, the {hemi}.aparc.stats file gives the 
thickness of several areas, one of them being the insula. Is it possible to get 
only the anterior insula thickness?

Thank you in advance, and I hope to hear from you soon.

Best,

Hanne van der Heijden



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Re: [Freesurfer] fspalm contrasts {Disarmed}

[Greve, Douglas N.,Ph.D.]

Oh, sorry, I did not include that as a possibility. FSL codes F-contrasts 
differently than t-contrasts (FS codes them in the same way, just a matrix). If 
you want to do it this way, you'll have to use PALM by itself without the 
fspalm frontend. fspalm should still create files that can be conveniently used 
in PALM, you'll just have to create the FSL-related files needed to run that 
contrast.

On 12/21/2020 6:56 AM, Marina Fernández wrote:

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Dear experts,



To correct multiple comparisons on the surface I'm using fspalm. I know that 
this command internally transforms the design contrast and desing matrix from 
the Freesurfer format to the fsl format so that FSL-PALM understands the input.

When the freesurfer contrasts include only one line, I can run permutations 
with fspalm without errors. The problem arises when the contrast has two lines 
(e.g., when including a three-level factor like in the example "Contrast 4: 
group.effect.mtx" from the link MailScanner has detected a possible fraud 
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https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V;
 or when including a two-way interaction between a dichotomic factor and two 
covariates of interest). You can see below the error. How can I solve this 
problem?



Thank you in advance.

Marina



**ERROR:**

Loading surface 1/1: 
/usr/local/freesurfer/subjects/amyloid74_thickness_average/surf/lh.white

Reading input 1/1: 
/usr/local/freesurfer/subjects/amyloid74_thickness_stats/smoothing/gaussians/lh.fsgd_subj_gauss003.mgh

Reading design matrix and contrasts.

Error using palm_vestread (line 56)

File not in the correct format: design.con



Error in palm_miscread (line 110)

[X.data,X.extra.PPH] = palm_vestread(X.filename);

Error in palm_takeargs (line 2111)

tmp = palm_miscread(opts.t{t},[],[],opts.precision);

Error in palm_core (line 33)

[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)

palm_core(varargin{:});



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Re: [Freesurfer] Error in selxavg3-sess {Disarmed}

[Greve, Douglas N.,Ph.D.]

Can you send the full terminal output? Do all subjects have the same paradigm 
files?

On 12/21/2020 5:24 AM, Nina Khatibi wrote:

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No, I have checked them all.

On Thu, Dec 17, 2020 at 6:05 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Are there presentations that are simultaneous?

On 12/12/2020 3:19 AM, Nina Khatibi wrote:

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Hi,
I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each 
subject contains 15 runs, I've done plenty of analyses with different paradigm 
files, but now with a paradigm file of 5 conditions, I face an error on subject 
22 run 12, which I can not solve.I wonder if you can help me.
I'm using macbook pro 2018, macOS Mojave 10.14.6 and 
freesurfer-darwin-macOS-7.1.1-20200811-8b40551


outanadir = 
/Volumes/ADATA/FunctionalData/Subject22/bold/fsaverage5Con2Sec.lh/pr012

Excluding 4 points

ERROR: fast_st2fir: two or more presentations are simultaneous

ERROR: creating FIR design matrix for Condition01

Dot indexing is not supported for variables of this type.


Error in flac_customize (line 354)

if(~isempty(flacnew.TFmtx))


Error in fast_selxavg3b (line 179)

flac = flac_customize(flac);



>> --

ERROR: fast_selxavg3() failed\n


Regards,

Nina




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Re: [Freesurfer] how to use recon-all command

[Greve, Douglas N.,Ph.D.]

Try looking at our tutorials on how to get started
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
but you can start by running
recon-all -s your-first-subject -i T1.nii.gz -all


On 12/21/2020 4:03 AM, 1248742467 wrote:

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Hello, everyone
my freesurfer enviroment:
Last login: Mon Dec 21 16:45:53 2020 from 10.16.10.109
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/tj/application/freesurfer
FSFAST_HOME   /home/tj/application/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/tj/application/freesurfer/subjects
cd /home/tj/application/freesurfer/subjects
MNI_DIR   /home/tj/application/freesurfer/mni

I have a T1.nii.gz file, So where should I put this file in?
What's more, if I want to the output is in the input data file, how to set the 
recon-all command?



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Re: [Freesurfer] Can't find Mindboggle datasets

[Greve, Douglas N.,Ph.D.]

don't know, try asking the people at mindboggle

On 12/21/2020 3:40 AM, 1248742467 wrote:

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Hello, everyone
In mindboggle website, the data is freesurfer-output, But I just want to 
download the 101 source data, use recon -all command preprocess them by myself.
I don't know where to download the source datasets, If you know, please give me 
a link. Thanks

Looking forward to your reply



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Re: [Freesurfer] Converting a binary volume roi.nii file to a label for roi analysis in Freesurfer

[Greve, Douglas N.,Ph.D.]

Run recon-all on the MNI template, then view your ROI on the output volume, 
including the surfaces to verify that the surfaces pass through your ROI. Map 
the ROI to the surface using mri_vol2surf with the --regheader option, then map 
the surface-ROI to each subject with mris_apply_reg (make sure to use the 
--no-rev) option, then run mri_segstats something like
mri_segstats --i lh.thickness --seg  roi-in-this-subject.mgz --id 1 --sum 
subject/stats/roi.stats
Then you can run asegstats2table with --statsfile=roi.stats -m mean to get a 
table across your subjects

On 12/20/2020 5:36 PM, Paul Dhami wrote:

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Dear Freesurfer community,

I have a volumetric roi.nii file created with spm, based on MNI coordinates 
from the literature.

My goal is to do a roi analysis in Freesurfer, as I am interested in 
correlating the thickness values of this roi with a behavioral measurer.

However, I am lost as to how I can appropriately convert this volumetric 
roi.nii file to a label.

I hate to ask for too much, but can anyone briefly share the commands or steps 
as to how to convert this roi.nii file to a label so I can conduct an roi 
analysis within Freesurfer?

Thank you very much,
Paul



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Re: [Freesurfer] error in running tkregisterfv

[Greve, Douglas N.,Ph.D.]

tkregisterfv requires an LTA file. Try running bbregister with an LTA output, 
eg,
bbregister --s subject_30_8_2020 --mov 
subject_motion_corrected_func_4D_RestingState.nii --reg 
affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.lta --init-header –bold



On 12/20/2020 5:03 AM, Peter de Best wrote:

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What am I trying to do:
I am trying to register my functional resting state scan to the MPRAGE scan 
(which is saved in the freesurfer subjects directory under ‘subject_30_8_2020’ 
after running recon-al on a MPRAGE that was aligned to AC PC). The mgz file 
brain.mgz and the functional scan aligned.

What are the commands I use
bbregister --s subject_30_8_2020 --mov 
subject_motion_corrected_func_4D_RestingState.nii --reg 
affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.dat --init-header –bold

tkregisterfv --mov subject_motion_corrected_func_4D_RestingState.nii --reg 
affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat –surfs

(bbregister works, tkregisterfv does not; I only provide the bbregistercode for 
context)

What is the error?
When I try to run tkregisterfv, I get the following output:
“cd /Users/me/Documents/30_8_2020/subject_REST_CF
freeview -transform-volume -viewport cor -v 
/Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/mri/orig.mgz:visible=0:name=orig.mgz(targ)/Users/me/Documents/30_8_2020/subject_REST_CF/subject_motion_corrected_func_4D_RestingState.nii:name=subject_motion_corrected_func_4D_RestingState.nii(mov):reg=/Users/me/Documents/30_8_2020/subject_REST_CF/affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat
 --surface 
/Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/lh.white:edgecolor=yellow--surface
 
/Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/rh.white:edgecolor=yellow
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary 
operator expected
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'”

My platform:
macOS Mojave, version 10.14.6

There is no recon-al log.

What I tried to do/ checked:

1)   FSL is installed.

2)the fsvglrun text describes fsvgl as a necessary file, and I found that 
VirtualGL is supposed to contained that, and I tried to install that. It also 
says that FS_ALLOW_VGLRUN should be set to 1, but I have no idea how to do that.

3)make sure to reboot after every potential solution.
None of that worked/ resolved the issue.



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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Greve, Douglas N.,Ph.D.]

You can use the fix from my previous email or you can add the following line 
any were into the gtmseg.ctab file:
 29  Left-undetermined   135 206 235 0 3


On 12/18/2020 11:06 PM, Julie Ottoy wrote:

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Sorry I would like to correct my previous post. The subject also failed with 
PVC.
I see now that the issue is happening during the gtm seg stage where it gives 
the error: WARNING: segid   29 Left-undetermined tissue type is not set.
For your information: I ran the standard FS and petsurfer pipeline as outlined 
on the wiki. I tried two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm --subseg-cblum-wm

Thank you for your help,
Julie

On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:

External Email - Use Caution

Dear Doug,

I have the same issue as the people below. I was wondering if this was solved 
in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got 
the following error in only one of my subjects. When I ran the same subject 
with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz 
--default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o 
/gtmnopvc.output.ceregrey --rescale 8 47
sysname  Linux
hostname -
machine  -
user -
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Any suggestions would be appreciated!
Thank you,
Julie

Re: [Freesurfer] mri_gtmpvc error: failed tissue type 
check
2017-11-25
 
Thread
 Douglas 
Greve

sorry, can you send me the details again?


On 11/21/17 10:24 AM, Klein, Gregory wrote:

Hello Donatas and Douglas,

Did you ever find a cause and solution for this problem? I too
occasionally get this error message, and cannot get the results of
mri_gtmpvc for certain subjects.


Any suggestions are welcome.
Thanks,
Greg

--
Gregory Klein, PhD
Principal Scientist, Biomarker Experimental Medicine Leader
F. Hoffmann-La Roche Ltd.
Bldg 01, Floor 16, N445
Grenazacherstrasse 170,
4070 Basel, Switzerland
Mobile: +41 79 572 97 89
Office Phone: +41 61 682 07 59
email: gregory.kl...@roche.com

Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City,
AL7 1TW Registration No:100674


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the information contained in this message is prohibited.


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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Greve, Douglas N.,Ph.D.]

Try adding
--replace 29 2
to your command line

On 12/18/2020 12:07 AM, Julie Ottoy wrote:

External Email - Use Caution

Dear Doug,

I have the same issue as the people below. I was wondering if this was solved 
in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got 
the following error in only one of my subjects. When I ran the same subject 
with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz 
--default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o 
/gtmnopvc.output.ceregrey --rescale 8 47
sysname  Linux
hostname -
machine  -
user -
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Any suggestions would be appreciated!
Thank you,
Julie

Re: [Freesurfer] mri_gtmpvc error: failed tissue type 
check
2017-11-25
 
Thread
 Douglas 
Greve

sorry, can you send me the details again?


On 11/21/17 10:24 AM, Klein, Gregory wrote:

Hello Donatas and Douglas,

Did you ever find a cause and solution for this problem? I too
occasionally get this error message, and cannot get the results of
mri_gtmpvc for certain subjects.


Any suggestions are welcome.
Thanks,
Greg

--
Gregory Klein, PhD
Principal Scientist, Biomarker Experimental Medicine Leader
F. Hoffmann-La Roche Ltd.
Bldg 01, Floor 16, N445
Grenazacherstrasse 170,
4070 Basel, Switzerland
Mobile: +41 79 572 97 89
Office Phone: +41 61 682 07 59
email: gregory.kl...@roche.com

Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City,
AL7 1TW Registration No:100674


Confidentiality note: This message is intended for the use of the
named recipient(s) only and may contain confidential and / or
privileged information. If you are not the intended recipient, please
contact the sender and delete this message. Any unauthorized use of
the information contained in this message is prohibited.


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Re: [Freesurfer] error message when running mri_info

[Greve, Douglas N.,Ph.D.]

You can see that the vox_units are Unknown in the fslhd output. This is the 
source of the problem in FS.

On 12/18/2020 10:53 AM, Jonathan Lynn wrote:

External Email - Use Caution

Hello,

I've been using a software to process SWI data that includes an option to save 
the output as nifti files. When I attempt to use either the mri_info or 
mri_convert commands on these nifti files I receive the following error message:

niiRead(): unknown space units 7 in /pfc/common_area/high_pass_1750_1910.nii

Where "high_pass_1750_1910.nii" is the name of my nifti file. This leads me to 
believe there is a problem in how my SWI processing software saves nifti files 
which makes them incompatible with FreeSurfer. I am curious if it is a problem 
with some aspect of the nifti header information that is causing me to receive 
this error and if so, which aspect?

Using the fsl program fslhd I have gotten the header info for one of these 
nifti files and pasted it below:

filename   high_pass_1750_1910.nii

sizeof_hdr 348
data_type  INT16
dim0   4
dim1   232
dim2   256
dim3   176
dim4   1
dim5   0
dim6   0
dim7   0
vox_units  Unknown
time_units rad/s
datatype   4
nbyper 2
bitpix 16
pixdim00.00
pixdim11.00
pixdim21.00
pixdim31.00
pixdim40.00
pixdim5-nan
pixdim66445431373862396660923732403945472.00
pixdim76445014188069157487771091399081984.00
vox_offset 352
cal_max3253932511416847943508928692748288.
cal_min0.
scl_slope  0.00
scl_inter  6444907725225778945067450074398720.00
phase_dim  0
freq_dim   0
slice_dim  0
slice_name Unknown
slice_code -99
slice_start30622
slice_end  -1814
slice_duration 0.00
time_offset0.00
intent Unknown
intent_code73
´õtent_nameëh`0
intent_p1  0.00
intent_p2  6444907725225778945067450074398720.00
intent_p3  68507965883187986432.00
qform_name Unknown
qform_code 0
qto_xyz:1  1.00  0.00  0.00  0.00
qto_xyz:2  0.00  1.00  0.00  0.00
qto_xyz:3  0.00  0.00  1.00  0.00
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Left-to-Right
qform_yorient  Posterior-to-Anterior
qform_zorient  Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1  0.00  0.00  0.00  0.00
sto_xyz:2  0.00  0.00  0.00  0.00
sto_xyz:3  0.00  0.00  0.00  0.00
sto_xyz:4  0.00  0.00  0.00  0.00
sform_xorient  Unknown
sform_yorient  Unknown
sform_zorient  Unknown
file_type  NIFTI-1+
file_code  1
descrip
aux_file   ¤ô

I am hoping someone can help me understand why I am receiving this error from 
mri_info.

Thank you,
John




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Re: [Freesurfer] Extracted mean timecourse from FS label {Disarmed}

[Greve, Douglas N.,Ph.D.]

Sorry, I don't know the best way to test it. You might ask the fmriprep people

On 12/18/2020 7:05 AM, Mason Wells wrote:

External Email - Use Caution

Hi Doug,

The waveforms look OK to me but was worried that the message was suggesting the 
command was not suitable with GIFTI data. Is there a way I can double check I'm 
good to carry on with the extractions?

Cheers,
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Tel: 02920 879628

Web: Cardiff University 
webpage<https://secure-web.cisco.com/1LQzzNf-MzUrTr2hGnNCunoDeWI5nr5U6ruKx_nFYsW0tBMMKOPAYKq1cvrf_s2Oi5K-X8byablEbTNgeAVpr9VNr1dhxKL2oUitSBnPSwQ0Af-cAPOgFH7V2VEVbPt97iF_fLPTmO3R4VkcrLTQU4V_o4lGSGnFYYJX7fLnLstaAe-pEUb7VySlJ7j7JbkDZ9m_eoot_wgEBwJZz2N_R4tl59ohgBv0lQIfP3LiNRcqN4IOe5sfksFSonJYbjt0mGdF73sEadTVDyosPNWcXMg/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214->

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>

Ffôn: 02920 879628


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, December 17, 2020 2:20 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Extracted mean timecourse from FS label

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.


I don't know, that msg probably comes from the gifti code we link to. It looks 
like it is just a warning. Do the output waveforms look ok?

On 12/9/2020 6:05 AM, Mason Wells wrote:
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Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

[Greve, Douglas N.,Ph.D.]

Is the lh.orig surface changing?

On 12/17/2020 5:53 PM, Ben Deen wrote:

External Email - Use Caution

Hi all,

I'm encountering an issue with surface reconstruction quality in ventromedial 
prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted 
input data to recon-all. I'm using the following command, with Freesurfer 7.1.1 
running on Mac OS 10.15.7 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551; the 
options file specifies "mris_inflate -n 30"):

recon-all -s ${subject} -i T1w.nii.gz -all -hires -expert ${optsFile} -T2 
T2w.nii.gz -T2pial

Across four participants I've tested with this approach, there is a consistent 
reconstruction issue with the gyrus rectus and medial orbital gyrus, in which 
they are cut off in the white and pial surfaces (see images at MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://www.dropbox.com/sh/crpcjro63bc6477/AADNtt9xJL1SV2kiaVJsGnSYa?dl=0;
 it's particularly clear against the T2 image). I've tried to correct the issue 
by manually modifying wm.mgz to include all wm voxels in these gyri. However, 
when I do so and rerun autorecon2-wm, the orig surface improves to incorporate 
the edits to wm.mgz, but the white/pial surfaces do not. By debugging 
individual steps of recon-all, I've found that the -white step seems to be to 
blame for this: when I rerun this step, the output white.preaparc surface 
doesn't change to incorporate my edits to wm.mgz.

Any thoughts as to what might be causing these issues - both the initial 
reconstruction problem, and the failure to update with manual edits? There is 
some signal dropout in the T1 image in this region, which may contribute to the 
issue, although I would hope the T2 image could compensate for this.

Thanks,

Ben



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Re: [Freesurfer] Multiple Frames

[Greve, Douglas N.,Ph.D.]

What are the 2 frames? You could extract the first or the second or average 
them or compute an RMS, but it depends on what is there

On 12/17/2020 2:03 PM, Hsieh, Stephanie wrote:
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Re: [Freesurfer] FREESURFER AND NEURONAVIGATOR IMAGE

[Greve, Douglas N.,Ph.D.]

Sorry, we don't have anything that will do this. I know there are a few out 
there that will do it, but I don't know their names off hand. Maybe 3D slicer.

On 12/17/2020 4:20 AM, marco.m...@tin.it wrote:

External Email - Use Caution

 I need to use freesurfer brain_anat.nii T1  and path.pd.nii (CST  WM tract ) 
in the navigator for neurosurgery. It is necessary to merge the two volume 
images and to transform it in dicom.
Exist a command for that or a procedure in Fressurfer? Or same other software?
Thanks!



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Re: [Freesurfer] fspalm error : --sig2p-max unknown

[Greve, Douglas N.,Ph.D.]

You need the patch. See the docs here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm under Setting Up

On 12/16/2020 2:02 PM, Marina Fernández wrote:

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Dear experts,

When I was running permutations with fspalm an error appeared because it 
couldn't find the --sig2p-max option when using mri_surfcluster internally.  
You can find below the terminal output.

How can I fix this error?

Thank you in advance
Marina.

 *Terminal output:
...
>> >> palm processing complete - running the surface cluster analysis...
/usr/local/freesurfer/subjects/merchi182_thickness_stats/stats/thickness/permutation/lctx/across/across_age_cov_none_0.05/pos/lh.fsgd_subj_gauss003/palm
mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject 
merchi182_thickness_average --hemi lh --annot aparc --sum 
contrast.clustertable.summary --no-fixmni --surf white --ocn contrast.ocn.mgz 
--oannot ./contrast.ocn.annot --sig2p-max
ERROR: Option --sig2p-max unknown
error: mri_surfcluster failed
fspalm --glmdir 
/usr/local/freesurfer/subjects/merchi182_thickness_stats//stats/thickness/permutation/lctx/across//across_age_cov_none_0.05/pos//lh.fsgd_subj_gauss003
 --cft 1.301 --name palm --iters 100 --cwp .05 --onetail: Signal 127
ans =
   255



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Re: [Freesurfer] Error During Fix Topology and Brain Usability

[Greve, Douglas N.,Ph.D.]

I don't think it is worth doing a surface-based analysis on this subject. The 
subcortical may be salvageable

On 12/16/2020 11:55 AM, Angel Hammond wrote:

External Email - Use Caution

Dear Experts,

I have a brain that I have been getting an error for during fix topology during 
recon-all using Freesurfer 6.0 on macOS Catalina. I have read a couple of 
threads on this same kind of error on the Freesurfer list and it seems this is 
due to some error in wm segmentation, cerebellum, or skull. However, being new 
with Freesurfer I am not sure what to check and how to fix such a large defect 
(or if it's even worth fixing - is this usable?). Just a few notes on this 
scan, it has heavy motion and was flagged by our radiologist as having 
'excessive white matter changes'. I uploaded the subject to the FTP named 
'088.tar.gz' to take a look at. Thank you!


The recon-all.log error message here:

INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-788 (nv=159056, nf=319688, ne=479532, g=395)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
101024 ambiguous faces found in tessellation
segmenting defects...
166 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
  -merging segment 8 into 3
  -merging segment 14 into 3
  -merging segment 48 into 3
  -merging segment 7 into 4
  -merging segment 6 into 5
  -merging segment 1 into 10
  -merging segment 20 into 16
  -merging segment 19 into 18
  -merging segment 10 into 23
  -merging segment 32 into 29
  -merging segment 37 into 30
  -merging segment 75 into 45
  -merging segment 62 into 64
  -merging segment 109 into 92
  -merging segment 127 into 92
  -merging segment 128 into 92
  -merging segment 141 into 92
  -merging segment 159 into 92
  -merging segment 157 into 92
  -merging segment 125 into 121
  -merging segment 123 into 122
  -merging segment 139 into 133
144 defects to be corrected
0 vertices coincident
reading input surface 
/study3/midus3/data/freesurfer/subjects/088/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -9.4365  (-4.7182)
  -vertex loglikelihood: -6.8975  (-3.4488)
  -normal dot loglikelihood: -3.5115  (-3.5115)
  -quad curv  loglikelihood: -6.1828  (-3.0914)
  Total Loglikelihood : -26.0283

CORRECTING DEFECT 0 (vertices=115, convex hull=128, v0=113)
After retessellation of defect 0 (v0=113), euler #=-112 (102634,295350,192604) 
: difference with theory (-141) = -29

CORRECTING DEFECT 1 (vertices=43, convex hull=79, v0=2438)
After retessellation of defect 1 (v0=2438), euler #=-111 (102656,295448,192681) 
: difference with theory (-140) = -29

CORRECTING DEFECT 2 (vertices=3335, convex hull=1683, v0=2597)
XL defect detected...
After retessellation of defect 2 (v0=2597), euler #=-113 (103831,299911,195967) 
: difference with theory (-139) = -26

CORRECTING DEFECT 3 (vertices=108, convex hull=48, v0=2938)
After retessellation of defect 3 (v0=2938), euler #=-111 (103837,299955,196007) 
: difference with theory (-138) = -27

CORRECTING DEFECT 4 (vertices=1336, convex hull=711, v0=3387)
XL defect detected...
After retessellation of defect 4 (v0=3387), euler #=-109 (104350,301857,197398) 
: difference with theory (-137) = -28

CORRECTING DEFECT 5 (vertices=162, convex hull=218, v0=4667)
After retessellation of defect 5 (v0=4667), euler #=-108 (104432,302198,197658) 
: difference with theory (-136) = -28

CORRECTING DEFECT 6 (vertices=18, convex hull=48, v0=5608)
After retessellation of defect 6 (v0=5608), euler #=-107 (10,302251,197700) 
: difference with theory (-135) = -28

CORRECTING DEFECT 7 (vertices=562, convex hull=419, v0=5682)
L defect detected...
After retessellation of defect 7 (v0=5682), euler #=-106 (104704,303262,198452) 
: difference with theory (-134) = -28

CORRECTING DEFECT 8 (vertices=44, convex hull=101, v0=5705)
After retessellation of defect 8 (v0=5705), euler #=-105 (104716,303339,198518) 
: difference with theory (-133) = -28

CORRECTING DEFECT 9 (vertices=37, convex hull=38, v0=8189)
After retessellation of defect 9 (v0=8189), euler #=-104 (104719,303364,198541) 
: difference with theory (-132) = -28

CORRECTING DEFECT 10 (vertices=180, convex hull=169, v0=8978)
After retessellation of defect 10 (v0=8978), euler #=-103 
(104772,303609,198734) : difference with theory (-131) = -28

CORRECTING DEFECT 11 (vertices=12, convex hull=25, v0=9633)
After retessellation of defect 11 (v0=9633), euler #=-102 
(104774,303621,198745) : 

Re: [Freesurfer] How to remove clusters less than 50 vertex/voxels in FreeSurfer during visualisation

[Greve, Douglas N.,Ph.D.]

You can add --minarea XXX to your mri_surfcluster command line where XXX is the 
minimum area in mm2

On 12/15/2020 8:33 AM, Sunil Khokhar wrote:

External Email - Use Caution

Dear Experts!

After doing the statistics I want to remove clusters that are less than 50 
voxels/vertices from sig.mgh file which contains the visualisation of the 
results. Looking forward to your advices.

Thanks in advance!



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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

[Greve, Douglas N.,Ph.D.]

Hard to say without the recon-all.log file, but my guess is that something is 
wrong with one of your surfaces. Load the surfaces in freeview and see how they 
look

On 12/14/2020 7:30 PM, Boa Sorte Silva, Narlon wrote:

External Email - Use Caution

Hi there,
Hope this finds you well

I have noticed the following error for some of my runs:


@# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020
/Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri
\n mris_volmask --aseg_name aseg.presurf --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1

It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon




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Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

[Greve, Douglas N.,Ph.D.]

There have been some changes that are breaking your stream. Try this

cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri
setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz 
--threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o 
../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg 
--no-rip-wmsa --no-rip-freeze --no-rip-lesion

If that works, then add this to your xopts file
 WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze 
--no-rip-lesion

On 12/14/2020 5:35 PM, Koch, Erin M. wrote:

External Email - Use Caution

Hi all,

The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 
from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use 
a series of shell scripts (that call freesurfer) which we successfully used to 
run to create flatmaps for non-human primate sessions.  I am stuck when using 
recon-all to inflate the surface.  Specifically, I am running the command:
 "recon-all -autorecon2-wm \
-subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\
-noaseg \
-mprage \
-xopts-use\
-debug\"
This step runs for quite some time, seemingly making progress and then "Exits 
with errors" .  In the terminal the error message that I can see is: "ERROR: 
need seg for ripping".  This is followed by: "recon-all - s SUBJECTNAME exited 
with ERRORS."  (Screen shot of this error is attached).  I will also attach the 
recon-all.log.

This issue does not seem to be a problem of quality of skull stripping or white 
matter segmentation, as the session can be completed with the older version of 
freesurfer, adn I get the same error with different sessions and subjects.  Can 
you please shed some light on this? The machine I am using is running Linux 
3.10.0-1127.18.2.e17.x86_64 .

As an aside -  Do you have any references or outline for flat map creation 
(specifically for non-human primates) with the newer versions of Free surfer? 
It is possible adapting our old pipeline is not ideal / there are more 
efficient or "better" ways to do this now.

Thank you for your help.

Best,

Erin



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Re: [Freesurfer] asegstats2table

[Greve, Douglas N.,Ph.D.]

If you use mris_anatomicalstats to create the stats file (in the stats folder), 
then use aparcstats2table to create a table from multiple subjects

On 12/11/2020 6:57 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

Hello Freesurfers, I have a question about the command asegstats2table. I want 
to obtain the structural data of a group set based on labels created by myself. 
I see that this is possible with mris_anatomicalstats for 1 subject but can I 
obtain the data for all my subjects in some way like asegstats2table using my 
labels?



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Re: [Freesurfer] group analyses

[Greve, Douglas N.,Ph.D.]

yes, run mris_preoproc with --meas volume, then surf2surf. Then run

mri_segstats --i lh.volume.mgz --exludeid 0 --seg ocn.mgz --avgwf avgwf.dat 
--accumulate

where lh.volume.mgz is the output of rerunning mris_preproc above
ocn.mgz is the ocn file which is output from the cluster analysis
avgwf.dat will be a number of subjects by number of clusters matrix with the 
volume foreach subject/cluster combination

On 12/7/2020 10:43 AM, Sara Lyn wrote:

External Email - Use Caution

Hi FS developers,

I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) 
for a surface based thickness group analysis. I am trying to extract volume 
measures from the same significant thickness ROIs. Is there any way to do this? 
Thank you!

Sara



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Re: [Freesurfer] group analyses {Disarmed}

[Greve, Douglas N.,Ph.D.]

Sorry, I'm not sure what you mean when you say the volume map is  uncorrected

On 12/14/2020 10:02 AM, Sara Lyn wrote:

External Email - Use Caution

And also i'm trying to extract these values from the uncorrected maps not 
corrected. Is there a way for that? Thank you

On Mon, Dec 14, 2020 at 9:59 AM Sara Lyn 
mailto:saralyn...@gmail.com>> wrote:
Hi
Thank you for your response. How do I correct this extracted volume for 
intracranial volume (etiv)?

Thank you

Sara

On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
When you run the thickness analysis with multiple comparisons correction 
(mri_glmfit-sim), it will create "ocn" files. These will be clusters of the 
significant areas. You can use this to extract other information. If you want 
volume, then run mris_preproc using the --meas volume flag, the apply the ocn 
to this file using mri_segstats using the --avgwf and --accumulate flags (and 
--exclude 0). This will give you a nsubjects-by-nclusters text file where each 
entry is the volume for that subject/cluster

On 12/8/2020 10:48 AM, Sara Lyn wrote:

External Email - Use Caution

Hi Joceyln,

I'm not trying to run a new group analysis but want to extract volume values 
from significant thickness ROIs obtained from a thickness group analysis.

Thank you

Sara

On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. 
mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,

You may want to try --meas volume in place of --meas thickness when running 
mris_preproc.

I would also recommend looking at our ROI 
Analysis<https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0>
 tutorial and Volumetric Group 
Analysis<https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529>
 tutorial. Please let us know if you are still having trouble.

Cheers,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sara Lyn mailto:saralyn...@gmail.com>>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group analyses


External Email - Use Caution

Hi FS developers,

I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) 
for a surface based thickness group analysis. I am trying to extract volume 
measures from the same significant thickness ROIs. Is there any way to do this? 
Thank you!

Sara
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Re: [Freesurfer] group analyses {Disarmed}

[Greve, Douglas N.,Ph.D.]

If you want to apply etiv correction when extracting the cortical volume with 
mris_preproc, just add --etiv to the command

On 12/14/2020 9:59 AM, Sara Lyn wrote:

External Email - Use Caution

Hi
Thank you for your response. How do I correct this extracted volume for 
intracranial volume (etiv)?

Thank you

Sara

On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
When you run the thickness analysis with multiple comparisons correction 
(mri_glmfit-sim), it will create "ocn" files. These will be clusters of the 
significant areas. You can use this to extract other information. If you want 
volume, then run mris_preproc using the --meas volume flag, the apply the ocn 
to this file using mri_segstats using the --avgwf and --accumulate flags (and 
--exclude 0). This will give you a nsubjects-by-nclusters text file where each 
entry is the volume for that subject/cluster

On 12/8/2020 10:48 AM, Sara Lyn wrote:

External Email - Use Caution

Hi Joceyln,

I'm not trying to run a new group analysis but want to extract volume values 
from significant thickness ROIs obtained from a thickness group analysis.

Thank you

Sara

On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. 
mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,

You may want to try --meas volume in place of --meas thickness when running 
mris_preproc.

I would also recommend looking at our ROI 
Analysis<https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0>
 tutorial and Volumetric Group 
Analysis<https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529>
 tutorial. Please let us know if you are still having trouble.

Cheers,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sara Lyn mailto:saralyn...@gmail.com>>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group analyses


External Email - Use Caution

Hi FS developers,

I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) 
for a surface based thickness group analysis. I am trying to extract volume 
measures from the same significant thickness ROIs. Is there any way to do this? 
Thank you!

Sara
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Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3

[Greve, Douglas N.,Ph.D.]

The GPU stuff may or may not work. It was hard to maintain because the GPUs 
kept changing so much, and it would not surprise me that the code from 5.3 is 
incompatable with GPUs today. But it looks like the error is that it could not 
find a file. Does that file actually exist?

On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote:

External Email - Use Caution

Hi!
I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am 
getting a strange error that I would love to get your input on:  cannot find 
freesurfer/average/RB_all_2008-03-26.gca
Neither the file nor the path exist.

This is the entire input and output:

recon-all -s hum_14600_parallel -i 
/neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221

Driver : 10.0
Runtime : 5.0

Acquiring CUDA device
Using default device
CUDA device: Tesla K40m


 === NUMBER OF OPENMP THREADS = 1 ===
stable5

NVIDIA driver version info:
NVRM version: NVIDIA UNIX x86_64 Kernel Module  410.79  Thu Nov 15 10:41:04 CST 
2018

ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca

Is there some documentation on how to set up the environment beyond 
LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the 
-use-gpu flag.

Thank you! Caspar




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Re: [Freesurfer] Error in selxavg3-sess

[Greve, Douglas N.,Ph.D.]

Are there presentations that are simultaneous?

On 12/12/2020 3:19 AM, Nina Khatibi wrote:

External Email - Use Caution

Hi,
I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each 
subject contains 15 runs, I've done plenty of analyses with different paradigm 
files, but now with a paradigm file of 5 conditions, I face an error on subject 
22 run 12, which I can not solve.I wonder if you can help me.
I'm using macbook pro 2018, macOS Mojave 10.14.6 and 
freesurfer-darwin-macOS-7.1.1-20200811-8b40551


outanadir = 
/Volumes/ADATA/FunctionalData/Subject22/bold/fsaverage5Con2Sec.lh/pr012

Excluding 4 points

ERROR: fast_st2fir: two or more presentations are simultaneous

ERROR: creating FIR design matrix for Condition01

Dot indexing is not supported for variables of this type.


Error in flac_customize (line 354)

if(~isempty(flacnew.TFmtx))


Error in fast_selxavg3b (line 179)

flac = flac_customize(flac);



>> --

ERROR: fast_selxavg3() failed\n


Regards,

Nina




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Re: [Freesurfer] HCP_1200 parcellation problems

[Greve, Douglas N.,Ph.D.]

Sorry, I can't tell from your email what the problem is. Can you elaborate?

On 12/9/2020 2:30 PM, najme soleimani wrote:

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Dear FreeSurfer Developers,
I downloaded the HCP_1200 subjects' structural extended data. I am attempting 
to have equal sized parcellation on scale 100, so I used parcellation results 
of Desikan atlas and increased the parcels from 68 to 100.
after obtaining split file, I run the following commands on FreeSurfer:
mris_divide_parcellation subj lh aparc.annot splitfile Desikan100
mris_divide_parcellation subj rh aparc.annot splitfile Desikan100
mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o 
$SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz
The interesting part is that after running this command some disconnectivity 
were seen in the parcels as it is shown in the picture. In 3D view, also, when 
the parcels were loaded on dsi studio, there were some holes on the parcels 
which  caused disconnected parcels.
I will appreciate if you help me to solve this problem.


kind regards,
Najme



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Re: [Freesurfer] need assistance to decode QDEC results

[Greve, Douglas N.,Ph.D.]

It depends on the order that you specified them. You will have four groups
SczUrban
SczRural
HVUrban
HVRural

The interaction will be of the form
(SczUrban-SczRural)-(HVUrban-HVRural)

Look in the y.fsgd to see what the  order of the classes is. You can then look 
in the contrast folder at C.dat to get the + and - 1s used in the contrast.

On 12/9/2020 12:58 PM, vittal korann wrote:

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Dear FreeSurfer experts,

I was running group interaction (for diagnosis and birthplace) in QDEC with 
gyrification as a dependent variable and age, gender as nuisance factors.
In diagnosis, we have 2 groups: i) schizophrenic patients ii) healthy 
volunteers.
Similarly, birthplace has 2 groups: i) urban ii) rural birth

For the above-said design, I got reddish yellow color results in the display 
tab of Qdec.
So, my query is that do results indicate that patients who were born in urban 
have a higher gyrification index than healthy volunteers who born in urban or 
something else? Do I sound correct in decoding the interaction results? If not 
please let me know the exact meaning of the results.

Looking forward to hearing from you.

Thanks,
Vittal




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Re: [Freesurfer] MP2RAGE pial surface edit error

[Greve, Douglas N.,Ph.D.]

Essentailly, this is a skull strip error, so you may need to remove the skull 
(ie, non-brain) manually

On 12/9/2020 6:25 AM, Elisa Rehbein wrote:

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Dear Freesurfer experts,

we are currently running  recon-all for our MP2RAGE images, using Freesurfer 7. 
However, when trying to edit pial surface errors and re-running (recon-all 
-autorecon-pial -subjid) it does not adjust the surface for some participants 
and leaves a black space (see picture attached). For denoising the salt and 
pepper noise in the background we used the script provided by (Marcques et al. 
2010). We are very confused as to why this may be happening for some subjects, 
as the background noise seems to be removed equally for all subjects. Do you 
maybe have suggestions for us on how to solve this problem? Many thanks in 
advance!


Kind regards,

Elisa



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Re: [Freesurfer] Extracted mean timecourse from FS label

[Greve, Douglas N.,Ph.D.]

I don't know, that msg probably comes from the gifti code we link to. It looks 
like it is just a warning. Do the output waveforms look ok?

On 12/9/2020 6:05 AM, Mason Wells wrote:

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Hi Experts,

I have pre-processed some resting-state date using fMRI prep. I have the 
functional data on the fs_native surface in bold.func.gii format for each 
hemisphere. I have created some FS labels and I would like to extract the mean 
time course from vertices within these labels. Is it possible to use FreeSurfer 
tools to do this? I have a feeling mri_segstats might be the correct option, 
but I don't believe this can be used with GIFTI functional data. I tried the 
command below


  *   mri_segstats --slabel sub-0006 lh 
/home/masontwells/Documents/freesurfer/subjects/sub-0006/label/lh.wang2015atlas.V1v.label
 --avgwf out.dat --id 1 --i 
../../post-fmriprep/sub-0006_ses-1_task-rest_acq-TR2000_space-fsnative_hemi-L_bold.func.gii

However, the terminal produces serval of these messages when the command runs:

  *   ** DA[599] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be 
NIFTI_INTENT_POINTSET)

I assume this is a sign that the command and data format are not compatible? If 
this is the case, can you advise on the best way to extract the mean time 
courses from my functional data? Will I have to resample the volume data to the 
surface with mri_vol2surf to get it into MGH format and then run mri_segstats?

Best wishes,
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University 
webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628




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Re: [Freesurfer] labels in the surface

[Greve, Douglas N.,Ph.D.]

This might be the way it is given that the AAL is volume-based and you are 
trying to put it on the surface. What is your vol2surf command?

On 12/10/2020 6:59 AM, Alberto Del Cerro Leon wrote:

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Hello Freesurfer team
With your help i obtained a AAL atlas on the surface and 1 label for each 
region. However, when I load the label into the inflate image, I obtain 
something like the one submitted in this e-mail. I expected a solid ROI on the 
surface to obtain the volume, curvature, etc of the entire region. It's 
something wrong? I am loading the label in an incorrect way?

The image represent the label of the anterior cingulate into the inflated image



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Re: [Freesurfer] Computing thickness from woT2.pial surfaces

[Greve, Douglas N.,Ph.D.]

If you're using v7XX, then you can use mris_place_surfaces. Look in the log 
file for the command line.

On 12/9/2020 6:15 AM, Antonín Škoch wrote:

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Dear experts,

I have processed my data with -T2pial option. I would like now to also compute 
thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a 
comannd which does the trick, without running recon-all -pial (which rewrites 
current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer 
version 6.0.

Thank you in advance,

Antonin Skoch




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Re: [Freesurfer] Does segmentation depend on input orientation {Disarmed} {Disarmed}

[Greve, Douglas N.,Ph.D.]

How did you change the orientation?

On 12/9/2020 4:16 AM, Nederpelt, D. van (David) wrote:
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Re: [Freesurfer] question about PVC of PETSurfer {Disarmed}

[Greve, Douglas N.,Ph.D.]

This is explained in the PETsurfer documentation. Can you be more specified 
about what that documentation does not cover?

On 12/9/2020 1:45 AM, 蒋袁芳 wrote:

External Email - Use Caution

Thanks for the reply, and we are still curious about the files that the 
Petsurfer out put. We want to know not only how to use the image after PVC, but 
also where to find the 3D image in the folder?
On 11/30/2020 01:14，Greve, Douglas 
N.,Ph.D.<mailto:dgr...@mgh.harvard.edu> wrote：
It is not set up to use the subfields. In principle it could be, but I don't 
think it would be very accurate because the subfields are so small.

On 11/17/2020 4:27 AM, 蒋袁芳 wrote:

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Hello Freesurfer,
We know that the freesurfer7 has given a new module to separate hippocampal 
subfields in MRI image, but we encoumter problems in registering the PET image 
with MRI image. We find that the resolution radio of PET image is not enough, 
it made the SUVr of hippocampal subfield we get is not accurate. So we want to 
use the PVC function of PETSurfer. Whether the PETsurfer output the result of 
PET image after PVC ? so that we can use it directly to registering with MRI 
image. If it doesn't output the result, can we save it in some ways? Thank you 
for your guidance.



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Re: [Freesurfer] Correct for sulcuses & ventricles size

[Greve, Douglas N.,Ph.D.]

On 7/11/2018 11:37 AM, John Anderson wrote:

External Email - Use Caution

Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of atrophy. Looking into the individual scans, the subjects 
are largely different in the space between the sulcuses and the size of 
ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
analysis?
What kind of correction? I'm not sure I understand what the problem is.
2. Including eTIV covariate does it help in this case?
No, since the skull does not change with atrophy
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the subjects?
See #1

I appreciate any advice,
John



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Re: [Freesurfer] inflated surface with holes

[Greve, Douglas N.,Ph.D.]

Ths is a topological error that can be fixed with mris_fix_topology. But this 
does not look human ...

On 12/8/2020 3:34 PM, Jie Zhao wrote:

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Hello Freesurfer Team


I have some questions about the inflated surface.  As is shown in the attached 
pictures, there are one big hole and three small hole on the right hemisphere, 
one big hole on the left hemisphere.  Could anyone give me some suggestions to 
handle it.

If you need any files, please let me know.


Thanks in advance!

Jie Zhao



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Re: [Freesurfer] recon-all error {Disarmed}

[Greve, Douglas N.,Ph.D.]

Does it work on other subjects? I'm guessing this has to do with having the MNI 
tools properly installed. For testing purposes, can you download and run 
version 7 to see if it works?

On 12/8/2020 12:40 PM, Devanshi jain wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to convert my .nii files (taken from ADNI dataset) to subject 
files (like bert). For the same I'm following this website : MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
I'm getting an error while performing step 4 of 'Running Freesurfer' heading.
Command that is giving error : recon-all -all -subjid 
Here my  is subject_0295

Error on the terminal : recon-all -s subject_0295 exited with ERRORS at Tue Dec 
 8 18:25:40 IST 2020

The freesurfer/subjects/subject_0295/scripts/recon-all.log file didn't mention 
any specific error.

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one? Also, I have attached the 
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Ubuntu 16.04.7 LTS
3) recon-all.log: see attached


--
Regards,
Ms. Devanshi Jain



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Re: [Freesurfer] group analyses {Disarmed}

[Greve, Douglas N.,Ph.D.]

When you run the thickness analysis with multiple comparisons correction 
(mri_glmfit-sim), it will create "ocn" files. These will be clusters of the 
significant areas. You can use this to extract other information. If you want 
volume, then run mris_preproc using the --meas volume flag, the apply the ocn 
to this file using mri_segstats using the --avgwf and --accumulate flags (and 
--exclude 0). This will give you a nsubjects-by-nclusters text file where each 
entry is the volume for that subject/cluster

On 12/8/2020 10:48 AM, Sara Lyn wrote:

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Hi Joceyln,

I'm not trying to run a new group analysis but want to extract volume values 
from significant thickness ROIs obtained from a thickness group analysis.

Thank you

Sara

On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. 
mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,

You may want to try --meas volume in place of --meas thickness when running 
mris_preproc.

I would also recommend looking at our ROI 
Analysis
 tutorial and Volumetric Group 
Analysis
 tutorial. Please let us know if you are still having trouble.

Cheers,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sara Lyn mailto:saralyn...@gmail.com>>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group analyses


External Email - Use Caution

Hi FS developers,

I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) 
for a surface based thickness group analysis. I am trying to extract volume 
measures from the same significant thickness ROIs. Is there any way to do this? 
Thank you!

Sara
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Re: [Freesurfer] convert to native space

[Greve, Douglas N.,Ph.D.]

On 12/5/2020 2:16 AM, Wei Shao wrote:

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Hello, Freesurfer team

This is Wei Shao, I was trying to convert the freesurfer automatic segmentation 
of the hippocampus subfield into native space so I can compare it with the 
manual segmentation.

Here is the command:
mri_label2vol --seg lh.hippoAmygLabels-BAYX-T2.v21.CA.mgz --temp rawavg.mgz 
--o lh.hippo-BAYX.mgz --regheader aseg.mgz

1 Could you tell me which files I should use in terms of the temp and regheader 
flag.
Template is fine, but use lh.hippoAmygLabels-BAYX-T2.v21.CA.mgz for 
--regheader

2 the manual segmentation based on T2 image, do I need to use the same T2 image 
as the overlaid image when it comes to Freeview? I think the nu.mgz is T1 
image, could you tell me where I can find the T2 image accordingly?
I'm not sure what you mean here.

3 do you know any command that can help me to check the information of the .mgz 
file like the 3dinfo command?
Try mri_info

I really appreciate your help, Thanks.

Best,
Wei





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Re: [Freesurfer] PVE correction tool Petsurfer {Disarmed}

[Greve, Douglas N.,Ph.D.]

They smooth by 8mm post processing and do allow you to have the unsmoothed 
images? Sigh. The best thing to do is to use sqrt(psf1^2+psf2^2) where psf1 is 
the psf of the scanner and psf2 is 8mm. psf1 is probably about 6mm. Which 
version of ADNI is this?

On 12/4/2020 5:42 PM, Julie Ottoy wrote:

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Dear FreeSurfer Team,

I am interested in the answer to the question of Subin below. I don't think 
this question was answered -- at least I cannot find the reply.
If the PET images are already smoothed to 8mm (which is the case with the 
post-processed ADNI images), does it make any sense to apply PVC with --psf 8 
at all on them?

The issue is that ADNI data does not provide the PSF of their scanner/recon 
method. As such, I am unsure what to do in this case.

Thank you for your help!
Best regards
Julie

Re: [Freesurfer] PVE correction tool on Freesurfer 
6

Lee Subin 
Kristine
 Wed, 20 Jul 2016 02:29:17 
-0700

Hi Doug,


Thanks for your help!

For your response to question #1 from my previous email(copied below), then if
all PET images were smoothed so that they all have a uniform resolution of 8mm
FWHM, would I put 8 for the psf flag?


> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.


Also, for the second question (copied below), then does setting it to .01 mean
maximum sensitivity to gray matter in each PET voxel, and thus this is the
recommended threshold for the most accurate resutls?


> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.



Best,

Subin


보낸 사람: Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> 대신
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
보낸 날짜: 2016년 7월 19일 화요일 오전 10:28:42
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6


the response is in the body f the mail

On 7/18/16 9:27 PM, Lee Subin Kristine wrote:

Hi Doug,

It seems that the email reply you just sent to me was empty. Could you please
check your email message again?


Thank you as always,

Subin



보낸 사람: Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
 대신

Re: [Freesurfer] flipped_hemisphere

[Greve, Douglas N.,Ph.D.]

Did you put a fiducial on your subject to mark left and right. If not, whey do 
you suspect the results are flipped? Did you use dicom file or did you convert 
them to something else before running recon-all?

On 12/3/2020 12:31 PM, Mora, Jocelyn S. wrote:
Hi,

If you are interested in checking information on the volume itself, try 
mri_info. If you would like specific examples for reference, I would recommend 
using our wiki pages.

Cheers,
Jocelyn

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

 on behalf of Edoardo Pinzuti 

Sent: Thursday, December 3, 2020 10:34 AM
To: Freesurfer support list 

Subject: [Freesurfer] flipped_hemisphere


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Hi,

after performing a segmentation with Freesurfer and making a Bem model it looks 
that some results are flipped between right and left hemispheres. Is there a 
way to check that Freesurfer is interpreting correctly the mri ?

Thanks



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Re: [Freesurfer] Does segmentation depend on input orientation {Disarmed}

[Greve, Douglas N.,Ph.D.]

Yes, this can happen  (and happens to almost all neuroimaging packages).  As 
with any optimization program, where it ends up depends a little on where it 
starts.

On 12/3/2020 6:31 AM, Nederpelt, D. van (David) wrote:
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Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

[Greve, Douglas N.,Ph.D.]

I've seen a lot of emails of this sort. Please try running it in matlab
y = load('yourroifile.txt')
X = load('glmdir/Xg.dat');
[beta rvar] = fast_glmfit(y,X);
C = load('glmdir/contrast/C.dat');
[F p] = fast_fratio(beta,X,rvar,C);

You'll have to include the matlab and fsfast/toolbox folders from 
FREESURFER_HOME in your matlab path


On 12/2/2020 8:11 PM, 李梦君 wrote:

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I extracted the value of the ROI average in each subject in the standard space 
and imported into the SPSS 26.0 to compute the significance of the difference.


-原始邮件-
发件人:"Greve, Douglas N.,Ph.D." 
<mailto:dgr...@mgh.harvard.edu>
发送时间:2020-12-02 23:31:26 (星期三)
收件人: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} 
{Disarmed} {Disarmed}

What are you using to compute the significance of the difference using the ROI 
average?

On 11/30/2020 7:59 PM, 李梦君 wrote:

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Yes, what should I do if there is something wrong


-原始邮件-
发件人:"Greve, Douglas N.,Ph.D." 
<mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-30 01:22:22 (星期一)
收件人: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} 
{Disarmed}

You mean that you are getting a different result between the voxel wise 
analysis and the ROI-wise analysis? And you created the ROI from the region 
that is significant in the voxel-wise analysis? If so, then I think something 
is wrong

On 11/17/2020 8:08 PM, 李梦君 wrote:

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I got the sum area and average area of the label, there is no significant 
difference between the mTBI group and health control, either.However, the label 
was significant different in the fsaverage between mTBI group and health 
control after multiple control. Did this correct?


-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-16 23:48:37 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

The lh_areapial.avgwf.dat has a value for each subject. That value will be 
whatever the y.mgh is. If you want a different value, then create a new y.mgh 
file. Also, I forgot to tell you to include --sumwf so that the avgwf file has 
the sum and not the average.

On 11/14/2020 5:24 AM, 李梦君 wrote:

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  I am sorry for that my presentation was not that good, the lh_areapial.sum and

lh_areapial.avgwf.dat file are uploaded, I get only one area value in the 
lh_areapial.sum file

with the following command.

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

My question was that how can I get the value of the area and volume in the 
standard space for every TBI and health control subjects.



-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-13 23:03:50 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed} {Disarmed}

sorry, I don't know what you are asking

On 11/12/2020 8:30 PM, 李梦君 wrote:

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Thanks! I get only one area value in the lh_areapial.sum file with this command:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

(1)Should I extract the area and volume one by one with the following command 
for each subject:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped 
to every subject from the fsaverage)
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0


-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-12 22:23:13 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed}

No, the area will be under the "Mean" column. Sorry, I know it is confusing. 
Also, you will just want to use the 2nd row.

Re: [Freesurfer] Aligning functional and structural scans with FsFast

[Greve, Douglas N.,Ph.D.]

Do you mean you want to register the fMRI data to the anatomical? If so, use 
bbregister. If you've run the fMRI through FEAT, then pass the template to the 
--mov flag

On 12/1/2020 10:46 PM, Karan Desai wrote:

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Hi FreeSurfer developers,

I have Freesurfer anatomical data from recon-all, and pre-processed functional 
data in NifTI format from FSL and you would like to use FsFast to align that 
data. What would be the best way to do that using FsFast? Is this possible?

Thanks.



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

[Greve, Douglas N.,Ph.D.]

What are you using to compute the significance of the difference using the ROI 
average?

On 11/30/2020 7:59 PM, 李梦君 wrote:

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Yes, what should I do if there is something wrong


-原始邮件-
发件人:"Greve, Douglas N.,Ph.D." 
<mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-30 01:22:22 (星期一)
收件人: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} 
{Disarmed}

You mean that you are getting a different result between the voxel wise 
analysis and the ROI-wise analysis? And you created the ROI from the region 
that is significant in the voxel-wise analysis? If so, then I think something 
is wrong

On 11/17/2020 8:08 PM, 李梦君 wrote:

External Email - Use Caution

I got the sum area and average area of the label, there is no significant 
difference between the mTBI group and health control, either.However, the label 
was significant different in the fsaverage between mTBI group and health 
control after multiple control. Did this correct?


-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-16 23:48:37 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

The lh_areapial.avgwf.dat has a value for each subject. That value will be 
whatever the y.mgh is. If you want a different value, then create a new y.mgh 
file. Also, I forgot to tell you to include --sumwf so that the avgwf file has 
the sum and not the average.

On 11/14/2020 5:24 AM, 李梦君 wrote:

External Email - Use Caution

  I am sorry for that my presentation was not that good, the lh_areapial.sum and

lh_areapial.avgwf.dat file are uploaded, I get only one area value in the 
lh_areapial.sum file

with the following command.

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

My question was that how can I get the value of the area and volume in the 
standard space for every TBI and health control subjects.



-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-13 23:03:50 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed} {Disarmed}

sorry, I don't know what you are asking

On 11/12/2020 8:30 PM, 李梦君 wrote:

External Email - Use Caution

Thanks! I get only one area value in the lh_areapial.sum file with this command:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

(1)Should I extract the area and volume one by one with the following command 
for each subject:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped 
to every subject from the fsaverage)
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0


-原始邮件-
发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-12 22:23:13 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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} {Disarmed} {Disarmed}

No, the area will be under the "Mean" column. Sorry, I know it is confusing. 
Also, you will just want to use the 2nd row. You can eliminate the first row 
with --exclude 0


On 11/12/2020 5:39 AM, 李梦君 wrote:

External Email - Use Caution

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
  MinMax   Range
  1   0161058 81037.1   Seg   242940.32810.7312 
0. 3.8885 3.8885
  2   1  2784 1182.3Seg00013760.6619 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

Re: [Freesurfer] mri_surf2surf lh.area does not match surface (148208, 146833)

[Greve, Douglas N.,Ph.D.]

It looks like you edited the subject but did not fully re-run it. Try
recon-all -s HLN-12-2 -autorecon3


On 12/1/2020 4:01 AM, 1248742467 wrote:

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Hello, Fs

When I run the following command:
mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trgsubject 
fsaverage5 --trgsurfval 
/home/tj/application/freesurfer/subjects/min_template/HLN-12-2-target/area 
--trg_type curv --hemi lh

the error message:
Reading curvature file 
/home/tj/application/freesurfer/subjects/HLN-12-2/surf/lh.area
ERROR: number of vertices in 
/home/tj/application/freesurfer/subjects/HLN-12-2/surf/lh.area does not match 
surface (148208,146833)

Not only the area, volume and jac.white have the same problems.
Do you know how to solve it?

Looking forward to your reply.



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Re: [Freesurfer] Fwd: Issue with custom label

[Greve, Douglas N.,Ph.D.]

Try --i mri/aparc+aseg.mgz instead of --c

On 11/30/2020 7:28 PM, Catherine Tallman wrote:

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Hello,

I was wondering if there were any updates on this question?

Thank you,
Catherine

-- Forwarded message -
From: Catherine Tallman mailto:ctall...@ucsd.edu>>
Date: Thu, Nov 19, 2020 at 8:57 AM
Subject: Issue with custom label
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

After running mri_vol2label I created a custom label named test.label. When I 
try to load the label onto lh.pial, I receive the following error: "Could not 
load label from ". The file is saved within the path folder itself. 
Within the terminal I receive the warning "label has not been mapped to 
surface". I was wondering what might be causing this issue? Attached is the 
label file.

mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.test.label

Thank you,
Catherine
--

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego


--

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego



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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Greve, Douglas N.,Ph.D.]

Yes

On 11/30/2020 10:45 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

Then, now that I have the AAL in the surface I should make a label for every 
region in the AAL_surface image with mri_vol2label with surf option and run 
mri_label2label for every label and every subject in my study. Is this the 
correct workflow?

El lun, 30 nov 2020 a las 16:26, Greve, Douglas N.,Ph.D. 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Oh, don't use .img as it cannot handle the surface dimensions. Technically, 
nifti cannot either, but I hacked our nifti version to accommodate. Or use mgh 
as you have done.

On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

First of all, thanks you Douglas for the support.
As I said i run the mri_vol2surf and I obtained an error:

mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI 
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target reference.
Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white
Done reading source surface
Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 104840
Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
Dim: 161783 1 1
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768

However I noticed that if i use the format .guii or .mgh this error message 
doesn't appear. Could I continue with the image in this format? What's the 
difference that makes this error appear with .img format?

El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Can you send the full terminal output?

On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:

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I tried to run mri_vol2surf with the following command: mri_vol2surf --src 
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi 
lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i obtain an error 
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768. How can i fix it?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Which MNI space? If mni152, then run recon-all on the mni152 template, then run 
mri_vol2surf with --regheader  mni152subjectname; also include --projfrac 0.5. 
But before you do that , load the AAL atlas onto the mni152subject with the 
surfaces to make sure everything aligns. You might want to do this with the 
colin27 brain instead because I think that is what the AAL atlas is defined on.

On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

Hello everyone, I tried to follow your instruction about how to get the 
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in 
the MNI space (i submit this image in the e-mail). Can I use this image in the 
mri_vol2surf? If so, i suppose that this image would be the input one, but i 
don't know what is registration file in the syntax of mri_vol2surf

Sorry for the inconvenience, Alberto



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Re: [Freesurfer] Multiple regression analysis

[Greve, Douglas N.,Ph.D.]

good question. I don't think there is anything wrong with multiplying two zs, 
but it might be more appropriate to multiply the raw covariates and then 
compute a z from that.

On 11/30/2020 4:07 AM, Marina Fernández wrote:

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Dear all,

I am doing a multiple regression analysis with 3 covariates of interest. I know 
that for testing two-way and three-way interactions I must create new variables 
by multiplying the covariates of interest. As Freesurfer transforms continuous 
variables to z score before applying statistic, is it correct to transform to z 
score the result of the previous multiplication? I am asking this because the 
result of multiplying two z transformed variables would be different.

Thanks a lot in advance.

Marina



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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Greve, Douglas N.,Ph.D.]

Oh, don't use .img as it cannot handle the surface dimensions. Technically, 
nifti cannot either, but I hacked our nifti version to accommodate. Or use mgh 
as you have done.

On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

First of all, thanks you Douglas for the support.
As I said i run the mri_vol2surf and I obtained an error:

mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI 
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target reference.
Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white
Done reading source surface
Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 104840
Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
Dim: 161783 1 1
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768

However I noticed that if i use the format .guii or .mgh this error message 
doesn't appear. Could I continue with the image in this format? What's the 
difference that makes this error appear with .img format?

El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Can you send the full terminal output?

On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:

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I tried to run mri_vol2surf with the following command: mri_vol2surf --src 
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi 
lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i obtain an error 
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768. How can i fix it?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Which MNI space? If mni152, then run recon-all on the mni152 template, then run 
mri_vol2surf with --regheader  mni152subjectname; also include --projfrac 0.5. 
But before you do that , load the AAL atlas onto the mni152subject with the 
surfaces to make sure everything aligns. You might want to do this with the 
colin27 brain instead because I think that is what the AAL atlas is defined on.

On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:

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Hello everyone, I tried to follow your instruction about how to get the 
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in 
the MNI space (i submit this image in the e-mail). Can I use this image in the 
mri_vol2surf? If so, i suppose that this image would be the input one, but i 
don't know what is registration file in the syntax of mri_vol2surf

Sorry for the inconvenience, Alberto



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Re: [Freesurfer] mri_surf2surf Cannot allocate memory

[Greve, Douglas N.,Ph.D.]

How was lh.sphere.reg created? It might be corrupted, so try creating it again.

On 11/30/2020 3:11 AM, 1248742467 wrote:

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Hello,Fs
When I used mri_surf2surf command to template the lh.thickness to fsaverage5 
space, the error appeared:
Command:
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv 
--trgsubject fsaverage5 --trgsurfval 
/home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/thickness
 --trg_type curv --hemi lh

Error message:
Reading source surface reg 
/home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/surf/lh.sphere.reg
TAGskip: tag=1601402226, failed to calloc 1931488256 bytes!


Do you know how to salve it? The memory is :
tj@bme01:~/application/freesurfer/subjects$ free
  totalusedfree  shared  buff/cache   available
Mem:  131673804 139816079091688241651183956   129212776
Swap:   8388604  169108 8219496

Looking forward to your reply.



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Re: [Freesurfer] what command can be used to template .vtk file to fsaverage5 space?

[Greve, Douglas N.,Ph.D.]

what space is the vtk surface in?


On 11/30/2020 2:55 AM, 1248742467 wrote:

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Hello, what command can map VTK file to fsaverage5 space? I want its vertex 
number to be 10242. If you know, please give me an example.
Looking forward to your reply



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Re: [Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

[Greve, Douglas N.,Ph.D.]

We don't have a centrum semiovale label in FS. You could try using the 
(Left,Right)-UnsegmentedWhiteMatter in the wmparc.mgz

On 11/27/2020 9:28 AM, miracle ozzoude wrote:

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Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and centrum 
semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) 
however, how do I extract the last one. What mask should I use to extract the 
centrum semiovale? I don't want to include the cerebellar white matter.

Thanks.

Best,
Paul



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Re: [Freesurfer] Mean Curvature

[Greve, Douglas N.,Ph.D.]

I don't know. I've never seen this type  of analysis. I think with and without 
would be valid analyses, but they would be answering different questions, so, 
as the scientist doing the study, it is more up to you.

On 11/27/2020 8:56 AM, Letitia Schneider wrote:
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Re: [Freesurfer] mri_segstats question

[Greve, Douglas N.,Ph.D.]

what is your command line?

On 11/29/2020 2:55 PM, RENXI LI wrote:
>  External Email - Use Caution
>
> The WM was cropped out by applying a grey-matter mask in SPM, and I am trying 
> to extract non-zero voxels with mri_segstats.
>
> Best,
> Renxi
>
>> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. 
>>  wrote:
>>
>> I don't understand why WM was cropped out. What command were you trying
>> to use?
>>
>> On 11/18/2020 2:39 AM, RENXI LI wrote:
>>>  External Email - Use Caution
>>>
>>> Hi Freesurfer experts:
>>>
>>> I am trying to extract the mean-time series from the functional image using 
>>> mri_segstats. However, the cerebral white matter signals were cropped out 
>>> in my functional images, and the regions that I am trying to extract signal 
>>> from are close to the cerebral white matter that some voxels at the 
>>> boundary may not contain any signals. Is there any arguments in 
>>> mri_segstats that I can use to only extract voxels that has non-zero 
>>> time-series?
>>>
>>> Best,
>>> Renxi
>>>
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Re: [Freesurfer] monkey atlas D99

[Greve, Douglas N.,Ph.D.]

Use mri_label2vol to map the segmentation into the fMRI space, then use 
mri_segstats using the --avgwf option to get time courses. Run it with --help 
to get examples

On 11/26/2020 9:16 AM, Francesca Strappini wrote:

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Dear FreeSurfer experts,

I'm trying to use the monkey atlas D99. First, I registered the segmentation 
atlas to the monkey anatomy through bbregister. Now, I need to resample the 
segmentation to the functional data and extract the mean value from each 
functional run using the ROIs contained in the segmentation as masks. I suppose 
I should mri_segstats but I'm not sure how. Any suggestion?

Thank you
Francesca


--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: 
francesca.strapp...@weizmann.ac.il



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Re: [Freesurfer] error: MatrixMultiply: m1 is null {Disarmed}

[Greve, Douglas N.,Ph.D.]

Not in FS. Try using dcm2niix

On 11/26/2020 5:07 AM, John Papatriantafyllou wrote:

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Hi freesurfer exps,
last year a recieve dicom 3d as one file (300 dicoms one file)
Is there any program to unpack them or any other way to recon all
John


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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

No, you'll have to add it as a covariate. Or you can add --etiv when you run 
mris_preproc and it will divide the maps by the eTIV

On 11/25/2020 3:23 PM, Sara Lyn wrote:

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Hi Freesurfer experts,

I'm doing a surface based volume analysis and wanted to know if there was a 
flag to regress out eTIV in the model.

Thank you



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Re: [Freesurfer] Mean Curvature for whole hemisphere

[Greve, Douglas N.,Ph.D.]

No, probably just an oversight

On 11/25/2020 10:06 AM, Josue Luiz Dalboni Da Rocha wrote:
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Re: [Freesurfer] PETSurfer voxelwise statistic

[Greve, Douglas N.,Ph.D.]

Traditionally, MG analysis is only run on GM. In principle, it is possible to 
run it on WM, but we don't offer that as an option.

On 11/25/2020 8:16 AM, Boris Rauchmann wrote:

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Dear all,

How can I run a voxelwise statistic using grey and white matter uptake? 
mgx.ctxgm.nii.gz and the other files in output all only include gm as I 
understand.

My goal is to run whole brain volume-based analysis. Like in this example for 
subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz

Thanks,
Boris





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Re: [Freesurfer] Splitting a label region?

[Greve, Douglas N.,Ph.D.]

Try mris_divide_parcellation
Run with --help to get docs

On 11/25/2020 1:57 AM, Hyon, Justin J. wrote:
>  External Email - Use Caution
>
> Hello,
> I am wondering whether there is a way to split a labeled region in a volume 
> into 2 labels, perhaps by using the Freeview gui? I just need to roughly 
> split one region generated via one of the default atlases into 2 custom 
> labels. I tried using the tools in Freeview, but I can only seem to edit 1 
> layer of the volume at a time.
> Thank You!
>
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Re: [Freesurfer] group analysis

[Greve, Douglas N.,Ph.D.]

For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male, 
CMT-Female and not use gender as a variable. Try that. I would also normalize 
the age and thickness

On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote:

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Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between two 
groups regressing out cortical thickness, age and sex.
My FSGD file is:
GroupDescriptorFile 1
Title Func
Class HC
Class CMT
Variables  Age gender
Input fs_VF HC  46 Female
Input fs_RF HC 24 Female
...

My group.diff.mtx is:
1 -1 0 0 0 0 0

My command line:
 mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir

But unfortunately I get this wrong message:
RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=146.140350 (col 3)
 The scale is much different between columns 5 and 3, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same


Can you please help me?

Thank you very much
Raf



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Re: [Freesurfer] Manual ROIs in PETSURFER

[Greve, Douglas N.,Ph.D.]

It is, but it can be either easy or hard. The easy way is to draw it on 
gtmseg.mgz and add an entry into gtmseg.ctab. Probably, you should copy the 
gtmseg.{mgz,ctab} to a new file and edit that. Otherwise, you can edit, eg, 
apas+head.mgz, and pass that to gtmseg with the --head option. At some point, 
the the ctab will need to be updated or gtmseg will fail. We will be updating 
this part to make it easier in the next year.

On 11/23/2020 4:27 PM, Jessica Cooperrider wrote:

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Hello,

I would like to draw a volume of interest on T1 images and then evaluate 
metabolism changes in this region. Is this possible to accomplish using 
PETSURFER?

Thank you for your time,
Jess



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Re: [Freesurfer] mri_surf2surf (and mri_preproc) clarification

[Greve, Douglas N.,Ph.D.]

I think that would be ok, but I would run this instead

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type 
curv --cortex --trgsubject fsaverage5  --trgsurfval ./mgh/1001_lh_fs5_thick.mgh 
--trg_type mgh –fwhm-trg 10



On 11/23/2020 4:11 PM, Daniel Leopold wrote:

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Dear Freesurfer experts,

The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 
7th order icosahedron. Does it place the lh.thickness curv into freesurfer 
space, or is it still in the subject's native space (i.e., pre-transformation 
to the fsaverage template)?

I used a similar process to downsample subjects' thickness to fs5 resolution, 
which I then concatenated and used as input for PALM. What I'm now wondering is 
whether results may be due to misalignment between individual subjects because 
they were not transformed to the fsaverage template and space. Do the inputs 
below (-srcsurfval) need to be thickness.fsaverage.mgh (already mris_preproc'd 
in the recon-all pipeline) instead?

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type 
curv --cortex --trgsubject ico --trgicoorder 5 --trgsurfval 
./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10

**Note: My apologies if this re-posts, but it doesn't seem like my initial 
submission went through**


With gratitude,
Dan



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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Greve, Douglas N.,Ph.D.]

If you want a cluster table, then you will have to run mri_surfcluster on the 
output of the conjunction. Run it with --help and write back if you need more 
info

On 11/21/2020 10:03 AM, Paula Maldonado wrote:

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Dear Douglas,

Could you please tell me where can I find the cluster table?

Thank you,
Best regards,

Paula

Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:

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Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
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Dear experts,
I am running an fMRI experiment in which I have four conditions: two main 
conditions (condition A and condition B) and two respective control conditions 
(condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity for 
condition A relative to condition B, after subtracting out the activity for the 
respective control conditions. In other words, I would like to perform the 
following contrast:
(condition A - condition A control) - (condition B - condition B control)
Then I would like to have a map that shows the reverse contrast too:(condition 
B - condition B control) - (condition A - condition A control).

How do I do that?To obtain the first map: (condition A - condition A control) - 
(condition B - condition B control) I have tried with the mergecontrasts-sess 
function with the -conjunction flag and the OR option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
-contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh

where Contrast1= (condition A - condition A control) and Contrast2= (condition 
B - condition B control)
however the map I get is exactly the same as (condition A - condition A 
control), as if subtracting out Contrast 2 had no impact on the map.

Thanks,

Paula



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Re: [Freesurfer] PETSurfer

[Greve, Douglas N.,Ph.D.]

One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ...
Otherwise, you can run fscalc, eg,

fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o 
mgx.ctxgm.rescaled.nii.gz



On 11/20/2020 11:44 AM, Boris Rauchmann wrote:

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Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean 
intensity using PETSufer? Is there a command to use in mri_gtmpvc like 
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value for 
scaling the atlas based results in gtm.stats.dat but how can I easily scale the 
image?

Thanks,
Boris






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Re: [Freesurfer] Time required to run permutations

[Greve, Douglas N.,Ph.D.]

This might be a bug with the --bg option when 1 is specified. Try it without 
--bg or try it with 2 or more threads

On 11/20/2020 10:20 AM, Basavaraju, Rakshathi wrote:
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Re: [Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

[Greve, Douglas N.,Ph.D.]

It is probably easier to just run recon-all on the mni152, then use 
mri_segcentroids on aparc.a2009s to extract the centroids

On 11/20/2020 2:50 AM, Hengameh Marzbani wrote:

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Hello Freesurfer developers,




For the purpose of reporting ROIs in my article, I need a list of X Y Z 
coordinates in MNI space for all the labels in the Destrieux atlas. I came 
across a previous post with the following steps:

Step 1:
 mri_annotation2label --subject fsaverage --hemi lh --annotation
 aparc.a2009s --outdir ~/myproject/processed/tmp

Step 2:
mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel 
lh.G_pariet_inf-Supramar.label --sum 
~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar  --centroid --thmin 0 
--hemi lh --subject fsaverage --nofixmni





Q1: All the ROIs appeared to have identical MNI coordinates. what should I do?

Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels 
in aseg.stats ROIs, What should I change?




Thank you in advance,
Best regards,
Hengameh




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