Re: [Freesurfer] mri_label2label no registration difference

of Douglas N. Greve [dgr...@mgh.harvard.edu] Sent: Wednesday, August 15, 2018 6:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2label no registration difference Can you send the command lines you used? On 08/15/2018 05:54 AM, Yagmur Ozdemir 19 wrote: > > Ex

[Freesurfer] mri_label2label no registration difference

External Email - Use Caution Hello FreeSurfer experts, I want to compare the labels produced by two different registration methods in mri_label2label; either using the sphere or TAL space as an intermediate ( --regmethod). However I see that there is no difference between the

[Freesurfer] mri_volcluster not recognize --mindistance

External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that the option --mindistance is not recognized, even though this option is

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

/24/18 6:52 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized

Re: [Freesurfer] How to convert label to volume

External Email - Use Caution In --temp /home/zwj/SCH_immune/A00 you seem to be missing the last bit of the file name, like .mgz or .nii. This option passes the template volume you want the output volume to match. For the second question, you can load that annotation and the

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

be causing the system to fill the whole volume. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 [yozdemi...@amherst.edu] Sent: Tuesday, July 24, 2018 1:23 PM To: Freesurfer support list

[Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally

Re: [Freesurfer] loading multiple saved points

, July 16, 2018 5:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] loading multiple saved points Not in tksurfer/tkmedit. You can create a point list to be used in freeview. On 07/16/2018 10:50 AM, Yagmur Ozdemir 19 wrote: > > External Email - Use Caution > > Hell

[Freesurfer] loading multiple saved points

External Email - Use Caution Hello Freesurfer experts, I am wondering if there is any way I can load up multiple points I saved in tkmedit, in either viewing software at the same time. Each time I defined a point, I changed the edit.dat file's name so it would save as

Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

ndexed based on the order that they were loaded. See here for more details: https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference Cheers, Katie On Tue, Jun 19, 2018 at 11:13 AM, Yagmur Ozdemir 19 mailto:yozdemi...@amherst.edu>> wrote:

Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

Ozdemir 19 [yozdemi...@amherst.edu] Sent: Tuesday, June 19, 2018 9:13 PM To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎ Subject: [Freesurfer] differing display colors for 2+ labels in tksurfer External Email - Use Caution Hello freesurfer experts, I am aiming to view 3

[Freesurfer] differing display colors for 2+ labels in tksurfer

External Email - Use Caution Hello freesurfer experts, I am aiming to view 3 to 8 different labels on one flattened surface patch created in tksurfer. Even if I can manually select the color of first label, the next ones end up sharing the same color and I cannot seem to change

Re: [Freesurfer] averaging surface labels?

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] averaging surface labels? why do you need to go into the volume at all? If the labels exist on the surface in the format of an annotation file, then you can use annot2std On 3/16/18 3:08 PM, Yagmur Ozdemir 19 wrote: Hello FreeSurfer experts, I am trying to create

Re: [Freesurfer] isxconcat-sess error: trgsubject

] isxconcat-sess error: trgsubject isxconcat-sess assumes that you sampled all your subjects to the common surface (fsaverage). You will have to re-run selxavg3-sess using data on fsaverage. On 3/19/18 12:15 PM, Yagmur Ozdemir 19 wrote: Thank you for the help! root@ubuntu:~/local/freesurfer

Re: [Freesurfer] isxconcat-sess error: trgsubject

-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 wrote: Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess

[Freesurfer] isxconcat-sess error: trgsubject

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

[Freesurfer] averaging surface labels?

Hello FreeSurfer experts, I am trying to create a group average of labels defined on inflated surface, and so far I tried mri_label2vol which succesfully got the labels to volume space and binarized for averaging, however when I sample this back to the inflated surface of fsaverage, using

Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

] tksurfer/freeview vertex coordinates difference? Hi Idil we keep track of different kinds of RAS coordinates, which may not be the same (surface ras, scanner ras, etc...). cheers Bruce On Thu, 1 Mar 2018, Yagmur Ozdemir 19 wrote: > Hello FS experts, > > I am wondering if anyone

[Freesurfer] tksurfer/freeview vertex coordinates difference?

Hello FS experts, I am wondering if anyone knows why the same vertices' coordinates are shown slightly different when opened in freesurfer and tksurfer. I was checking some annotation files for each subject across the two on inflated surface, and noticed slight coordinate differences in RAS.

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file Try running selxavg3-sess with -monly sxa3.m Then start matlab and run sxa3.m On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote: > Dr. Greve, > > I tried with root access and it still gave the same error. I am using a

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

: [Freesurfer] fast_selxavg3.m error/analysis.info file I don't know, it is all very weird. What platform are you using? On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote: > Dr. Greve, > > Yes I have tried making new files. (I also gave the previous files and > folders full permission with chmod

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

analysis with a different name and just see if fails? On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote: > Hello Dr. Greve, > > The analysis.info file is below. I should also say that, when I am trying to > create new analysis and contrast files, while creating the .config file for > cont

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

me the analysis.info file? On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote: > Hello Dr. Greve, > > Yes it exists. The output below was with debug option. > > Best > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

8:51 AM, Yagmur Ozdemir 19 wrote: Hello FreeSurfer experts, I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following

[Freesurfer] fast_selxavg3.m error/analysis.info file

Hello FreeSurfer experts, I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output: #@# Sess05

Re: [Freesurfer] JRE error in fsfast/matlab

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] JRE error in fsfast/matlab By default the graphics are turned off when running selxavg-sess. I often see that error message, but it never ends up causing the program to terminate. Is your process terminating prematurely? On 12/13/17 10:24 AM, Yagmur Ozdemir 19

[Freesurfer] JRE error in fsfast/matlab

Hello FreeSurfer experts, I have been running into a matlab-related problem that I was wondering if anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run selxavg-sess command, the matlab tries to find the OpenGL

Re: [Freesurfer] % overlap of multiple labels

On Mon, 20 Nov 2017, Yagmur Ozdemir 19 wrote: > Dr. Fischl, > > Thank you for the suggestion, I believe a --label-list option still does a > one-on-one comparison but I will think about it. > Another question: in the annotation file option, does the script look at the &g

Re: [Freesurfer] % overlap of multiple labels

To: Freesurfer support list Subject: Re: [Freesurfer] % overlap of multiple labels Hi Idil I think you can use --label-list for multiple labels, or stuff them into annot files and it should do everything it finds. cheers Bruce On Fri, 17 Nov 2017, Yagmur Ozdemir 19 wrote: > Hello Freesurfer expe

[Freesurfer] % overlap of multiple labels

Hello Freesurfer experts, I am using the mris_compute_parc_overlap command to compute the % overlap of two labels of the same region. Is there a way to do this for multiple labels? Best Idil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] register.dof6.dat file missing with register-sess

, October 16, 2017 6:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] register.dof6.dat file missing with register-sess which version of FS are you using? Is this a new analysis done from scratch or had you preprocessed before? On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote: Hello

[Freesurfer] register.dof6.dat file missing with register-sess

Hello Freesurfer experts, After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the

Re: [Freesurfer] generating automatic functional label

Idil, I'm not going to plow through someone else's code:) If you want to summarize what it does, I might be able to figure out if we have something that does it. On 09/25/2017 03:21 PM, Yagmur Ozdemir 19 wrote: > Hello FreeSurfer developers, > > This is a piece of code I came across for pro

[Freesurfer] generating automatic functional label

Hello FreeSurfer developers, This is a piece of code I came across for producing a functional label with using time course estimates from MEG/EEG data, for freesurfer use. I am wondering if something similar is available to estimate a functional label/region from fMRI data with similar

Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

of Yagmur Ozdemir 19 [yozdemi...@amherst.edu] Sent: Thursday, September 21, 2017 12:16 AM To: Freesurfer support list Subject: Re: [Freesurfer] Matlab(?) failure in selxavg3-sess It says that it's not on the path. I thought export MATLAB would fix that issue but apparently not. Best, Idil

Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

...@nmr.mgh.harvard.edu] Sent: Wednesday, September 20, 2017 11:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Matlab(?) failure in selxavg3-sess what happens if you run the getmatlab command? If you don't have a startup.m, then create one On 09/20/2017 04:34 PM, Yagmur Ozdemir 19 wrote: > He

[Freesurfer] Matlab(?) failure in selxavg3-sess

Hello freesurfer experts, When I run the selxavg3-sess command (for retinotopy) , the command exits with this "fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt') if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end" and then

Re: [Freesurfer] mask alignment problem/mri_mask

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 [yozdemi...@amherst.edu] Sent: Thursday, August 17, 2017 7:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem

Re: [Freesurfer] mask alignment problem/mri_mask

to be able to help you. How did you create the mask? Why volume to you expect it to be in register with? What are the volumes MW_IIHC_aTAL.nii native.template.mgh and native.orientation.mgh ? Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > It seems to be in the right orientation

Re: [Freesurfer] mask alignment problem/mri_mask

...@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 6:50 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask sorry, I don't understand Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > Thank you! > > Then I guess I would use the volume as the transform file to c

Re: [Freesurfer] mask alignment problem/mri_mask

ri_convert -at to map the mask into the right coordinate system so that you can then view it in freeview to make sure it is correct cheers Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > The mask in volume format was created using a docker image and it works well > both with my f

Re: [Freesurfer] mask alignment problem/mri_mask

eers Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > A volume file I want to save as a mask(the orange/red shaded areas in the > picture) on top of my volume file does not align as seen in the picture. I > have used mri_vol2vol to align the

Re: [Freesurfer] mri_binarize/mri_mask command help

or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template? On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote: > > Dear FreeSurfer experts, > > I am trying to use the following command to merge the volume file of a > template w

Re: [Freesurfer] Talairach error

with -no-talcheck. On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote: > Hello FreeSurfer experts, > > I have been running into a consistent problem of Talairach alignment > error in my recon-all for some of my subjects, even though I was able > to get a completed recon-all for

Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote: > Hello FreeSurfer experts, > > I am trying to run recon-all on a nifti file converted from PAR/SEC using > dcm2niix, and this error came up pretty soon after the script started to > run; > > >> mri_convert.bin > /home/l

[Freesurfer] multi-frame input error with PAR/SEC origin file

Hello FreeSurfer experts, I am trying to run recon-all on a nifti file converted from PAR/SEC using dcm2niix, and this error came up pretty soon after the script started to run; >> mri_convert.bin >> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz >>

Re: [Freesurfer] creating mesh with specifications

that will do that. sorry Bruce On Mon, 31 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > I am trying to export an inflated surface file and its overlay made in > Freesurfer to a different software and it seems like the surface file needs > to have a >

[Freesurfer] creating mesh with specifications

Hello freesurfer experts, I am trying to export an inflated surface file and its overlay made in Freesurfer to a different software and it seems like the surface file needs to have a particular number of vertices, triangles and average # of neighbors to be compatible. I have used mris_decimate

Re: [Freesurfer] Segmentation Violation problem in surface files

] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > When I do either of the conversions with mris_convert, the system gi

Re: [Freesurfer] Segmentation Violation problem in surface files

...@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > When I do either of the conversions with mris_convert, the sys

Re: [Freesurfer] Segmentation Violation problem in surface files

over the surface (that is, they are one value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti cheers Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote: > I am trying to export the overlays in .mgz format to Brainvoyager wh

Re: [Freesurfer] Segmentation Violation problem in surface files

Idil, > > we only store surface overlays in .mgz not surfaces themselves. Try loading > a surface (like lh.inflated) then load whatever you were looking at as an > overlay on the surface > cheers > Bruce > On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote: > >> Hello freesurfer e

Re: [Freesurfer] Segmentation Violation problem in surface files

(like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > I am trying to use an occipital lobe template adapted to my data as several > surface and volume files, and

[Freesurfer] Segmentation Violation problem in surface files

Hello freesurfer experts, I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up; freadFloat: fread

Re: [Freesurfer] freeview command error

] freeview command error Hi Idil do you know what shell you are using in the terminal that you are trying to call freeview from? On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello, > I only followed the steps in the install/download page and installed tcsh > because it was not runn

Re: [Freesurfer] freeview command error

error Hi Idil how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello, >

[Freesurfer] freeview command error

Hello, I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject. lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you

[Freesurfer] problem in installation practices

Hello, I am testing my FreeSurfer installation by doing the practices shown on the page. Regardless of command-although I managed to convert the sample to nifti format- this error on line 2 shows up. Can anyone explain what that could be caused by and point me in the right direction to fix it?