*From:* freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[dgr...@mgh.harvard.edu]
*Sent:* Monday, March 19, 2018 5:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] isxconcat-sess error: trgsubject
Can you run
PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject
Can you run
mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz
for each of your subjects and send us the result?
On 3/19/18 7:52 AM, Yagmur Ozdemir 19
//mask.nii.gz
129873 1 1 1
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[dgr...@mgh.harvard.edu]
Sent: Monday, March 19, 2018 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] isxconcat
Can you run
mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz
for each of your subjects and send us the result?
On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer developers,
I am trying to concatenate session files of different subjects using
isxconcat-sess. I am not really
Hello Freesurfer developers,
I am trying to concatenate session files of different subjects using
isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will
fail unless all sessions are the same subject" pops up as I understand this is
what isxconcat-sess is meant to do, and
Hi Freesurfer experts,
I'm trying to concatenate subjects using the command
isxconcat-sess -d $SUBJECTS_DIR -sf
/cluster/roffman/users/Stable5_PerRun/Subject_Files/TEST -analysis
SIRP_LoadRegression_Stable5_072915 -c Cond2vFix -hemis -o
Hi Surfers and Doug,
I was trying to average two scan sessions of the same subject and
isxconcat-sess under dev-env failed again. This time I get this message:
ERROR: cannot find
Hi,
Does anyone know what has changed in isxconcat-sess command in
nmr-dev-env? Previously I could use it to average different sessions of
the same subject. But now I am getting this error:
INFO: trgsubject is self, this will fail unless all sessions are the same
subject
ERROR: cannot find
I just made a fix. Can you try it out and let me know if it works?
On 05/14/2015 11:38 AM, SHAHIN NASR wrote:
Hi,
Does anyone know what has changed in isxconcat-sess command in
nmr-dev-env? Previously I could use it to average different sessions
of the same subject. But now I am getting
Hi Doug,
It works without any error.
Thanks a lot
On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
I just made a fix. Can you try it out and let me know if it works?
On 05/14/2015 11:38 AM, SHAHIN NASR wrote:
Hi,
Does anyone know what has changed
I put it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess
If you just want to concatenate the vertex values, then just do
something like
mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz
sess2/bold/analysis/contrast/ces.nii.gz ...
On
You can mri_concat the cesvar files. For the dof, just add up the dofs
in each run.
On 04/27/2015 05:08 PM, Reza Rajimehr wrote:
If I use mri_concat instead of isxconcat-sess, will I have all the necessary
files for fixed-effects averaging by mri_glmfit? Specifically, can I generate
If I use mri_concat instead of isxconcat-sess, will I have all the
necessary files for fixed-effects averaging by mri_glmfit?
Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat
for --ffxdofdat in mri_glmfit?
Reza
I put it here:
Thanks Doug! Could you clarify a bit more on how to add up the dofs
in each run?
You can mri_concat the cesvar files. For the dof, just add up the dofs
in each run.
On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote:
If I use mri_concat instead of isxconcat-sess, will I have
Eachoutput.nii.gz sess1/bold/analysis folder will have a dof.dat file
with a number in it. Add up all those numbers, create a files with the
sum in it, and pass that file to mrI_gomfit.
On 04/27/2015 06:18 PM, Reza Rajimehr wrote:
Thanks Doug! Could you clarify a bit more on how to add up the
Thanks Doug! Could you put the updated isxconcat-sess script in an ftp
server and provide a link so that I can download it? I do not have
access to the dev environment.
Now I should run the command with the flag -trgsubject F99, right?
My analysis is on the surface, and I only want to
Hi,
I am trying to use isxconcat-sess for averaging functional data across two
monkeys. The data in two monkeys have been analyzed on a common surface
(F99). When I run this:
isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts
-o group2
I get an error:
ERROR: cannot find
Hi list,
I'm performing the FS-FAST analysis.
Some months ago, I have already preformed this analysis on some subjects
without problem.
Now, I have added some subjects. When I rerun the analysis i have these error:
for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast
Hi NewFei, canyou run the following commands and send me dng.log ?
cd /autofs/space/audrey_001/users/FSFASTFC
isxconcat0-sess -m pcc -o
matchedCTRLSCHIZ.rhDG.newest/noGMrhDGmc6/X/mni305.pcc.nii.gz -sf
matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -c X -a
noGMrhDGmc6 -split
There's a bunch of stuff in the analysis folder (noGMrhDGmc6) including
some .mat files. FSFAST sees these .mat files and thinks they are
contrasts. So, you can remove all the extra stuff in that folder or you
can spec the contrast with -contrast.
doug
On 01/25/2013 11:49 AM, New Fei Ho
It looks like that file is there now. Is the problem fixed?
doug
Chindhuri Selvadurai wrote:
Hi all,
When I run isxconcat-sess, I am experiencing an error finding a 'dof' file
in my analysis directories within the FSD files.
subjects directory: /cluster/manoach/milton/subjects
command
Hi all,
When I run isxconcat-sess, I am experiencing an error finding a 'dof' file
in my analysis directories within the FSD files.
subjects directory: /cluster/manoach/milton/subjects
command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c
type_v_rest_vol -o
Hi Krishna, if you have a proper freesurfer analysis and registration to
the anatomical, it should work fine.
doug
Krishna Srihasam wrote:
Hi,
Is there a way to use” isxconcat-sess” to average monkey fMRI data?
i.e. I have two groups of monkeys (say, test and control groups) and I
want
Hi,
Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e. I
have two groups of monkeys (say, test and control groups) and I want to do
group analysis on their data..
Regards,
krishna
___
Freesurfer mailing list
Hi,
Is there a way to use isxconcat-sess to average monkey fMRI data? i.e. I
have two groups of monkeys (say, test and control groups) and I want to do
group analysis on their data..
Regards,
krishna
___
Freesurfer mailing list
isxconcat-sess creates the files that you pass to mri_glmfit (ie,
multi-frame volumes and/or surfaces where each frame is a
subject). Something like:
AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii
You can then use this as input to mri_glmfit
Thanks Doug,
I was just a bit confused because I thought the help for mri_glmfit
mentioned an osgm directory that wasn't there.
I was given a matlab script that does that now.
I'm using a command like this:
mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask
../tal.mask.nii
What does your matlab script do? Your glmfit cmd looks fine.
On Thu, 15 Oct 2009, Maximilien Chaumon wrote:
Thanks Doug,
I was just a bit confused because I thought the help for mri_glmfit
mentioned an osgm directory that wasn't there.
I was given a matlab script that does that now.
I'm
Hi freesurfers,
I've been running isxconcat-sess with this line
chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf
subjlist.txt -analysis Analyse_Simple_Confidence -c
High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08
I was expecting to find a directory called osgm
Hi,
I've been running into a problem when trying to run a group analysis.
When I go to run isxconcat-sess, I use this command:
isxconcat-sess -sf hc.txt -df sesspar -analysis Ext -c CS+lvsCS-l -
percent -o ./HC-Ext-083109 -hemis -trgsubject fsaverage
It runs through the whole isxconcat
Hi Doug,
I just tried to type in the command you sent me in the dev environment
and got this error:
ERROR: Flag -talxfm unrecognized.
-a MR-sm6-stc -m mask -o
MR-group-allsubjects-sm6-stc/MR-sm6-stc/tal.masks.mgz -interp nearest -fsd
bold -talres 2 -talxfm fsl-ta1.xfm -sf
Hi,
I wanted to know if it's possible to run isxconcat-sess but have it use
a different talairach transform when it calls mri_vol2vol. Currently the
default is mri/transforms/talairach.xfm, but I want it to use one I had
outputted from a previous processing step -
I've just added something to do this. Add -talxfm fsl-tal.xfm to the cmd
line. Live on next dev update.
doug
Bill Monaco wrote:
Hi,
I wanted to know if it's possible to run isxconcat-sess but have it
use a different talairach transform when it calls mri_vol2vol.
Currently the default
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