[Freesurfer] ALLvsFIX contrast
Hi, In an fMRI experiment, I have 60 conditions. I want to make ALLvsFIX contrast to select vertices that are visually responsive, by finding vertices that have ces values greater than zero in this contrast. For this, I can run: mkcontrast-sess -analysis analysisname -contrast allvsfix -a 1 -a 2 -a 3 ... -c 0 Since this is a very long command, is there a smarter way to make such contrast? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess without fsaverage
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 /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
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 concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr wrote: > 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 > /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz > > Even when I add -trgsubject F99 to the command, I get the same error. > > How can I tell isxconcat-sess not to use fsaverage? > > I am using Freesurfer v5.3 stable. > > Thanks, > Reza > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
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: 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 Monday, April 27, 2015, Reza Rajimehr wrote: > 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 concatenate the vertex > values. I have an orig.mgz file in the mri subdirectory of F99, but I hope > isxconcat-sess does not ask for additional volume files. > > > Best, > > Reza > > > > I just fixed this for the dev environment. Try running it from there. > Though I think this is just the start of the problems. > doug > > > > On Monday, April 27, 2015, Reza Rajimehr > wrote: > >> 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 >> /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz >> >> Even when I add -trgsubject F99 to the command, I get the same error. >> >> How can I tell isxconcat-sess not to use fsaverage? >> >> I am using Freesurfer v5.3 stable. >> >> Thanks, >> Reza >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
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 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 > cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? > > > Reza > > > > 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 Monday, April 27, 2015, Reza Rajimehr > wrote: > >> 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 concatenate the vertex >> values. I have an orig.mgz file in the mri subdirectory of F99, but I hope >> isxconcat-sess does not ask for additional volume files. >> >> >> Best, >> >> Reza >> >> >> >> I just fixed this for the dev environment. Try running it from there. >> Though I think this is just the start of the problems. >> doug >> >> >> >> On Monday, April 27, 2015, Reza Rajimehr wrote: >> >>> 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 >>> /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz >>> >>> Even when I add -trgsubject F99 to the command, I get the same error. >>> >>> How can I tell isxconcat-sess not to use fsaverage? >>> >>> I am using Freesurfer v5.3 stable. >>> >>> Thanks, >>> Reza >>> >>> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04
Hi, Is there any plan by the Freesurfer team to address this well-known bug? http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html For now the only workaround is to enter values through command-line. Best, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04
Hi Bruce, I guess I will eventually move to freeview - though I am not quite sure if it is easy to use with FS-FAST. For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, except the one described below. So it would be great if this bug, that is specific for ubuntu, is resolved. Best, Reza Hi Reza can you use freeview for what you want instead? tksurfer and tkmedit are deprecated cheers Bruce On Thursday, June 11, 2015, Reza Rajimehr wrote: > Hi, > > Is there any plan by the Freesurfer team to address this well-known bug? > > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html > > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html > > For now the only workaround is to enter values through command-line. > > Best, > Reza > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04
Thanks Zeke! I have replicated this problem in at least three machines running Ubuntu 14.04. Reza Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that people post to the list about in order to attempt replicate. But I'll install Ubuntu 14 on a laptop after OHBM concludes and investigate. -Zeke On Friday, June 12, 2015, Reza Rajimehr wrote: > Hi Bruce, > > > I guess I will eventually move to freeview - though I am not quite sure if it > is easy to use with FS-FAST. > > > For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, > except the one described below. So it would be great if this bug, that is > specific for ubuntu, is resolved. > > > Best, > > Reza > > > > Hi Reza > > > > can you use freeview for what you want instead? tksurfer and tkmedit are > deprecated > > cheers > > Bruce > > > > On Thursday, June 11, 2015, Reza Rajimehr > wrote: > >> Hi, >> >> Is there any plan by the Freesurfer team to address this well-known bug? >> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html >> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html >> >> For now the only workaround is to enter values through command-line. >> >> Best, >> Reza >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04
Thanks Doug! What is the estimated time for the release of Freesurfer/FS-FAST stable version 6, including a documentation to use it with freeview? Reza The new version of fsfast will use freeview for tksurfer/tkmedit/tkregister. In 5.3, you can use tkmeditfv and/or add -freeview to the tkmedit-sess command line. I've put the 6.0 versions of tksurferfv and tksurfer-sess hereftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksurferfvftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksurfer-sess You can try copying them into your bin (make backup of tksurfer-sess) and seeing if they run. There might be some incompatibilities with freeview 5.3 doug On Friday, June 12, 2015, Reza Rajimehr wrote: > Hi Bruce, > > > I guess I will eventually move to freeview - though I am not quite sure if it > is easy to use with FS-FAST. > > > For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, > except the one described below. So it would be great if this bug, that is > specific for ubuntu, is resolved. > > > Best, > > Reza > > > > Hi Reza > > > > can you use freeview for what you want instead? tksurfer and tkmedit are > deprecated > > cheers > > Bruce > > > > On Thursday, June 11, 2015, Reza Rajimehr > wrote: > >> Hi, >> >> Is there any plan by the Freesurfer team to address this well-known bug? >> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html >> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html >> >> For now the only workaround is to enter values through command-line. >> >> Best, >> Reza >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04
Hi Zeke, I am wondering if you had a chance to look at this. Thanks, Reza Hello Reza, > > > I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but > exists only in Ubuntu 14. It's tough because we don't have test machines with > every Linux distro that people post to the list about in order to attempt > replicate. But I'll install Ubuntu 14 on a laptop after OHBM concludes and > investigate. > > > -Zeke > > > > On Friday, June 12, 2015, Reza Rajimehr > wrote: > >> Hi Bruce, >> >> >> I guess I will eventually move to freeview - though I am not quite sure if >> it is easy to use with FS-FAST. >> >> >> For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, >> except the one described below. So it would be great if this bug, that is >> specific for ubuntu, is resolved. >> >> >> Best, >> >> Reza >> >> >> >> Hi Reza >> >> >> >> can you use freeview for what you want instead? tksurfer and tkmedit are >> deprecated >> >> cheers >> >> Bruce >> >> >> >> On Thursday, June 11, 2015, Reza Rajimehr wrote: >> >>> Hi, >>> >>> Is there any plan by the Freesurfer team to address this well-known bug? >>> >>> >>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html >>> >>> >>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html >>> >>> For now the only workaround is to enter values through command-line. >>> >>> Best, >>> Reza >>> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Visualizing functional maps in tksurfer
Hi, Using anatomical parcellation, I have labels for the occipital and temporal lobes in my subject. I have a functional map in the same subject that I want to show the activity only in the occipital and temporal cortex, and I want to mask the activity in the other parts of the cortical surface. How can I do this with FS-FAST/Freesurfer? Thanks, Reza * Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] versus baseline in mkcontrast-sess
... and one more question: In the latest version of FS-FAST (v5.3), is there a difference between the following two: mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 -c 0 mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 I have blocks with no stimulus that I have specified them as 0 in the paradigm files. Thanks, Reza * Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Brodmann annotation on fsaverage
Hi, Freesurfer has an annotation file for Brodmann areas, which is ?h.PALS_B12_Brodmann.annot. This Brodmann parcellation doesn't seem to be accurate in certain regions (e.g. in retrosplenial and perirhinal cortex). Does anyone have an alternative Brodmann atlas that can be visualized in Freesurfer (i.e. on fsaverage)? We are particularly interested in medial structures in occipital, parietal, and temporal lobe. Best, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Order of overlays
Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Normalization of external regressors
In a functional analysis, we have a set of external regressors (e.g. mean luminance of stimuli, size of stimuli, etc.). Should we normalize values before including them in the regressor files? If so, what is the recommended way of normalization ... z-scoring? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Questions about beta.nii.gz
Hi, I have two questions: 1) In an fMRI experiment, we have 64 stimulus conditions and a baseline condition. All conditions are presented in each run. After running the analysis: mkanalysis-sess -a category.rh -surface self rh -fsd bold -fwhm 3 -event-related -paradigm paradigm_category.par -nconditions 64 -refeventdur 1 -TR 2 -polyfit 2 -spmhrf 0 -mcextreg -per-run -force selxavg3-sess -s subj1sess1 -a category.rh We load beta.nii.gz in Matlab. It has 131546 rows corresponding to the vertices in rh, and 118 columns. The first 64 columns correspond to the stimulus conditions that we have. I guess the next 6 columns correspond to the motion regressors. What are the remaining 48 columns? 2) When we run selxavg3-sess with -run-wise: selxavg3-sess -s subj1sess1 -a category.rh -run-wise We have a beta.nii.gz file for each run. But this time, each beta.nii.gz file has 70 columns. Why the number of columns here is different from that in the beta file generated without -run-wise? Thanks for shedding light on this issue! Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Two recons with different vertex coordinates
Hi, We have run recon-all twice on a single subject, both times without any error. Using a functional localizer, we have made a surface-based label for an ROI (FFA) in the ventral temporal cortex of the inflated surface from the first recon. When we visualize the same label on the inflated surface of the second recon, the label shows up as scattered points in the lateral parietal cortex! Why do we see such a huge difference in the vertex coordinates across the two recons of a single subject? Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Drawing a circle around a vertex on a surface
Hi, I want to draw a circle around a vertex on the smoothwm or pial surface, with a particular radius (e.g. 10 mm), fill the circular region and save it as a label file, then repeat this for all the vertices on the surface. I need this for doing a searchlight analysis. Does anyone have a script/code for it? I know that mris_pmake (using Dijkstra's algorithm) can be used for this purpose, but I don't know exactly how to make it to work in a script for drawing circular ROIs. Thanks for any help! Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Drawing a circle around a vertex on a surface
Thanks Doug! I also found another solution from you in this post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031726.html Reza One way is to create a surface overlay with the target vertex = 1 and other vertices 0 (mri_volsynth, use delta, works for surface overlays too). Then smooth by a certain FWHM (mri_surf2surf or mris_fwhm). This will create a circle. If you divide all vertices by the value of the vertex after smoothing and then threshold at 0.5, then you should have a circle of radius approximately FWHM/2. On Sunday, November 8, 2015, Reza Rajimehr wrote: > Hi, > > I want to draw a circle around a vertex on the smoothwm or pial surface, > with a particular radius (e.g. 10 mm), fill the circular region and save it > as a label file, then repeat this for all the vertices on the surface. I > need this for doing a searchlight analysis. Does anyone have a script/code > for it? > > I know that mris_pmake (using Dijkstra's algorithm) can be used for this > purpose, but I don't know exactly how to make it to work in a script for > drawing circular ROIs. > > Thanks for any help! > > Reza > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Convolving external regressors with HRF
During the functional analysis in FS-FAST, are the external regressors convolved with the hemodynamic response function? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Convolving external regressors with HRF
Hi Doug, Since our external regressors are stimulus-related (e.g. mean luminance of stimuli), we need to convolve them with a hemodynamic response function. In mkanalysis-sess, we have used -spmhrf 0 to model conditions. Is there a code or Matlab script for HRF convolution, so that we apply exactly the same spmhrf function for modeling the external regressors? Thanks, Reza No, they are not On 02/17/2017 05:09 PM, Reza Rajimehr wrote: >* During the functional analysis in FS-FAST, are the external regressors *>* convolved with the hemodynamic response function? *>>* Thanks, *>* Reza *>>>* ___ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> * -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Convolving external regressors with HRF
Thank you so much Doug! I just have one more question: Before convolving regressors with HRF, I looked at X matrix and noticed that the values of regressors have been changed/scaled. For example, the original values in a regressor file are: 134.8300 0 141.1200 0 91.5310 0 96.1870 0 But they have been apparently shifted by a constant value in the X matrix: 91.8168 -43.0132 98.1068 -43.0132 48.5178 -43.0132 53.1738 -43.0132 Why is there such a change in the regressor values? Thanks, Reza You can use the following matlab code. You can ignore the warning printed after the toepliz operation. The OriginalRegressor should be a vector of length Ntp, then write out the NewRegressor to a new external regressor file. TR=2; % seconds Ntp=100; t = TR*[0:Ntp-1]'; h = fast_spmhrf(t); a = zeros(Ntp,1); a(1) = 1; X = toeplitz(h,a); NewRegressor = X*OriginalRegressor; On 02/21/2017 04:02 PM, Reza Rajimehr wrote: >* Hi Doug, *>>* Since our external regressors are stimulus-related (e.g. mean *>* luminance of stimuli), we need to convolve them with a hemodynamic *>* response function. In mkanalysis-sess, we have used -spmhrf 0 to model *>* conditions. Is there a code or Matlab script for HRF convolution, so *>* that we apply exactly the same spmhrf function for modeling the *>* external regressors? *>>* Thanks, *>* Reza *>>* No, they are not *>>>* On 02/17/2017 05:09 PM, Reza Rajimehr wrote: *>* >/During the functional analysis in FS-FAST, are the external regressors />/convolved with the hemodynamic response function? />//>/Thanks, />/Reza />//>//>/___ />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> *>* <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> / *>* -- *>* Douglas N. Greve, Ph.D. *>* MGH-NMR Center *>* greve at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> *>* <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Phone Number: 617-724-2358 *>* Fax: 617-726-7422 *>>* Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> *>* <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> *>* FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> *>* www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> *>* <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> *>* Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> *>>>* ___ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> * -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] The sulc file from mris_inflate
Hi, We have used mris_inflate: mris_inflate rh.smoothwm rh.inflated The command generates inflated and sulc files. We would like to do a little bit of smoothing on the sulc file, so that we get rid of few scattered regions where small positive curvature islands are located within negative curvature areas (and vice versa). How can we achieve this? mris_inflate has two options: -n and -dist, but assigning different values for these options doesn't seem to have any effects. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] The sulc file from mris_inflate
Thanks Bruce! mri_surf2surf does not accept a curvature file as an input. So we are thinking to make a .nii file with curvature values and pass it to mri_surf2surf. In case you have a simpler solution, we would be happy to hear it. Best, Reza I think mri_surf2surf can be used to smooth the sulc on the surface (as opposed to changing the way that the inflation works) On Sun, Jun 11, 2017 at 11:52 PM Reza Rajimehr wrote: > Hi, > > We have used mris_inflate: > > mris_inflate rh.smoothwm rh.inflated > > The command generates inflated and sulc files. We would like to do a > little bit of smoothing on the sulc file, so that we get rid of few > scattered regions where small positive curvature islands are located within > negative curvature areas (and vice versa). How can we achieve this? > > mris_inflate has two options: -n and -dist, but assigning different values > for these options doesn't seem to have any effects. > > Thanks, > Reza > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] The sulc file from mris_inflate
You were right Bruce! mri_surf2surf worked for the curvature file. We needed to specify --src_type and --trg_type as curv. Best, Reza On Mon, Jun 12, 2017 at 12:52 PM Reza Rajimehr wrote: > Thanks Bruce! > > mri_surf2surf does not accept a curvature file as an input. So we are > thinking to make a .nii file with curvature values and pass it to > mri_surf2surf. In case you have a simpler solution, we would be happy to > hear it. > > Best, > Reza > > > I think mri_surf2surf can be used to smooth the sulc on the surface (as > opposed to changing the way that the inflation works) > > > > On Sun, Jun 11, 2017 at 11:52 PM Reza Rajimehr wrote: > >> Hi, >> >> We have used mris_inflate: >> >> mris_inflate rh.smoothwm rh.inflated >> >> The command generates inflated and sulc files. We would like to do a >> little bit of smoothing on the sulc file, so that we get rid of few >> scattered regions where small positive curvature islands are located within >> negative curvature areas (and vice versa). How can we achieve this? >> >> mris_inflate has two options: -n and -dist, but assigning different >> values for these options doesn't seem to have any effects. >> >> Thanks, >> Reza >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Mask and Label
Hi, I have two unrelated questions: 1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The masks might be overlapping. I want to make a new mask file in which vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and vertices that are 0 in all three masks get the value of 0. How can I do that? 2) I have a text file containing a list of vertices in a column format. How can I convert it to a label file? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Surface-based label to a mask
Hi, Is there an easy way to convert a surface-based label to a mask without going to Matlab? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ROI analysis in Matlab
Hi, For my dataset, it appears to be easier to do an ROI analysis in Matlab (instead of using funcroi commands). I just want to make sure the procedure described below is right: 1) I have a label/ROI on the right hemisphere surface of a subject (e.g. MT from the motion localizer). I convert it to a mask file (MT.mask.nii.gz). I load it to Matlab using MRIread. In an fMRI experiment, I have 3 conditions. For the right hemisphere vertices of the subject, I compute cespct.nii.gz for the contrasts of each condition vs. baseline (1_vs_0 , 2_vs_0 , 3_vs_0). Then I load the three cespct files to Matlab using MRIread. 3) For the vertices that are 1 in the MT.mask.nii.gz, I calculate the averaged cespct across those vertices, in each contrast. So I will have % signal change values for the three conditions. 4) I repeat this for all subjects and do statistics across subjects. Any comments? Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] An overwrite issue with selxavg3-sess
I have done a functional analysis for some contrasts using selxavg3-sess. In the contrast folders, I have added some files. Now I want to do the same analysis for some new contrasts. My guess is that selxavg3-sess computes all the contrasts again, and I am worried that the new folders overwrite the previous ones and I lose the files that I have manually added. If this is the case, is there a way to run selxavg3-sess for some specified contrasts? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Spatial smoothing in Matlab
Hi, For a simulation purpose, I want to load a surface into Matlab, assign a random value (taken from a normal distribution) to each vertex, do spatial smoothing on the surface with a given FWHM (e.g. 5mm), then do some computations with the smoothed values. I am wondering if there is a Matlab code that I can use for surface smoothing, similar to what FS-FAST preprocessing does in Freesurfer version 5 and above. Thanks, Reza * Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Spatial smoothing in Matlab
Thanks Doug! I need to do this procedure 100 times, so I have to automate it. Do you have an example C-shell script for this? Or is there a way to call mri_surf2surf inside a "for loop" of Matlab? Thanks, Reza not that I know of. When I have to do this, I save the data to a file, then call mri_surf2surf with a system call, then load the result back into matlab. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Individual commands in preproc-sess
Hi, I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis of monkey data. To have a better control on the parameters of the analysis, I prefer to run the individual commands of preproc-sess one-by-one and check the output of each stage before proceeding with the rest of preproc-sess. Specifically I may manually edit the functional-anatomical registration, so I want to check the registration before moving on to the next step in preproc-sess. Also I need to skip the human-specific aspects of the analysis (e.g. Talairaching) if there are such things in preproc-sess. So is there a list of individual commends, in an appropriate order, that are used in preproc-sess? If someone has a routine for monkey data analysis with FreeSurfer v5.3, I would be happy to know about that as well. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Change in the location/path and the name of subject
Hi, I have got anatomicals of a subject from someone else. The anatomicals have been processed, and the surfaces have been reconstructed. The path to these files in my machine is obviously different from the path where data have been analyzed. I also want to change the name of the subject and give a name based on a convention that I have for my other subjects. Would the change in the location and name of the subject be problematic later on when I want to work with the anatomical data or use them during the functional data analysis? (re-processing of the anatomicals is not an option, since these are monkey data with heavy amounts of manual editings) Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Using fieldmap to correct EPI distortions
Hi, I have a basic question, but the answer can be useful for others as well. I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So: My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan) My EPI data: fmc.nii.gz files in run folders Now I have three questions: 1) How can I unpack the fieldmap data? An example command ... 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful. 3) How will the undistorted volumes be used later on in the FS-FAST analysis stream? Your help would be very much appreciated. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using fieldmap to correct EPI distortions
I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration. > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > registration, I want to use fieldmap data to correct spatial distortions > of EPI data. So: > > My fieldmap data: dicom files from a fieldmap scan (there are actually two > series of dicom files for that scan) > > My EPI data: fmc.nii.gz files in run folders > > Now I have three questions: > > 1) How can I unpack the fieldmap data? An example command ... > > 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an > example command would be very useful. > > 3) How will the undistorted volumes be used later on in the FS-FAST > analysis stream? > > Your help would be very much appreciated. > > Thanks, > Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using fieldmap to correct EPI distortions
Hi Doug, So I am using a command like this: epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46 --esp 0.31 --sigma 2 --perev (note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because this command apparently does not have --o option) Before running the above command, I have registered the mag and phasediff volumes to the template volume and I have generated new volumes (fid_mag and fid_phasediff) that are already in register with the template. I have two steps remaining in preproc-sess, which are register-sess and rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two commands? I assume that when I use the above flag(s), my EPI fmc volumes will be dewarped first, and then they will get registered to the anatomical and the surface, right? So I hope that when I view/check the result of registration with tkregister2 (for possible manual interventions), I will see the dewarped template ...? Finally what is the effect of specifying -b0dc in mkanalysis-sess? Thanks, Reza > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > registration, I want to use fieldmap data to correct spatial distortions > of EPI data. So: > > My fieldmap data: dicom files from a fieldmap scan (there are actually two > series of dicom files for that scan) > > My EPI data: fmc.nii.gz files in run folders > > Now I have three questions: > > 1) How can I unpack the fieldmap data? An example command ... I think you get two series out, one magnitude and one phase, just convert those to nifti > > 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an > example command would be very useful. something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located) > > 3) How will the undistorted volumes be used later on in the FS-FAST > analysis stream? When you run preproc-sess and mkanalysis-sess add -b0dc to the command line > > Your help would be very much appreciated. > > Thanks, > Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] A question about spherical registration
Hi, I have a question about spherical registration, and I couldn't find a relevant answer in the mailing list. I have two subjects S1 and S2 with corresponding functionals. I want to show the functionals of each subject on the surfaces of the third subject S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg files yet because these are monkey subjects and I did not want to register them to the buckner40.tif template. Since my goal is not group averaging, and it is just to map functionals to the same-subject anatomicals and then to the target-subject anatomicals, I was thinking of one of the following solutions: 1) Convert sphere of S3 to a template .tif file, then use mris_register to register spheres of S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Not sure if mris_make_template works for one subject though. 2) Make a template from "S1 and S2" through the procedure described at https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingaregistrationtemplatefromscratch.28GW.29. Then register S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Which approach is recommended? BTW, I do not know of a monkey template that is based on the surfaces from a large group of monkeys. Thanks for any advice, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Converting GIFTI files to Freesurfer files
Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Converting GIFTI files to Freesurfer files
Hi, I tested this with mris_convert provided by Nick in the link below, and it worked fine. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ However, mris_convert in dev version gave me the segmentation fault (core dumped). Just FYI! Best, Reza Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] A question about spherical registration
Thank you Doug for your comprehensive response. This looks clear, and I am going to try it out. Just one question for now: In step 1 (create a template from a single subject), I do not yet have "sphere.reg". Should I write "--surf-reg sphere"? make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX On 09/19/2014 10:24 AM, Reza Rajimehr wrote: > Hi, > > I have a question about spherical registration, and I couldn't find a > relevant answer in the mailing list. > > I have two subjects S1 and S2 with corresponding functionals. I want to > show the functionals of each subject on the surfaces of the third subject > S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg > files yet because these are monkey subjects and I did not want to register > them to the buckner40.tif template. Since my goal is not group averaging, > and it is just to map functionals to the same-subject anatomicals and then > to the target-subject anatomicals, I was thinking of one of the following > solutions: > > 1) Convert sphere of S3 to a template .tif file, then use mris_register to > register spheres of S1, S2, and S3 to that template and generate > sphere.reg for all the subjects. Not sure if mris_make_template works for > one subject though. > > 2) Make a template from "S1 and S2" through the procedure described at > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingaregistrationtemplatefromscratch.28GW.29. > Then register S1, S2, and S3 to that template and generate sphere.reg for > all the subjects. > > Which approach is recommended? > > BTW, I do not know of a monkey template that is based on the surfaces from > a large group of monkeys. > > Thanks for any advice, > Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] A question about spherical registration
Hi Doug, Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was no obvious error for that on the screen. Not sure if this happened because of not having an annot file for mris_make_template. Here is what I saw on the screen: %% /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Wed Oct 1 23:00:55 EDT 2014 /home/reza/structurals setenv SUBJECTS_DIR /home/reza/structurals/ output ddir is /home/reza/structurals/ uid=1000(reza) gid=1000(reza) groups=1000(reza),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),108(lpadmin),124(sambashare) make_average_surface Wed Oct 1 23:00:56 EDT 2014 /home/reza/structurals /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere input subjects: F99 output subject: iter00 mri_add_xform_to_header -c auto /home/reza/structurals//iter00/mri/mni305.cor.mgz /home/reza/structurals//iter00/mri/mni305.cor.mgz INFO: extension is mgz #@# Making lh registration template - /home/reza/structurals/iter00 mris_make_template -norot -annot aparc lh sphere F99 lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject F99 (1 of 1) reading spherical surface /home/reza/structurals//F99/surf/lh.sphere... could not read annot file /home/reza/structurals//F99/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif %% Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] A question about spherical registration
Hi Doug, Before I saw your response, I modified make_average_surface code by removing -annot aparc flag in the mris_make_template command within this code, and my script worked fine all the way to the end without any error. The change you made in make_average_surface would be useful in future. Just a minor point: You have modified this part: set cmd = (mris_make_template -norot aparc \ $hemi $sphere_reg $SUBJECTS $atlas) if($UseAnnot) set cmd = ($cmd -annot) Not sure if aparc should be kept in the line ... Best, Reza It is trying to use the annotation when making the registration tif. This is hard coded in your version of make_average_surface. I've attached a new version. Run it with --no-annot. Let me know if it works and I'll check it into our distribution doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] rawfunc2surf-sess with a limited set of surface files
Hi, I want to use rawfunc2surf-sess to project the functional data onto the surface in the source subject and then in the target subject. My source subject has been processed in Freesurfer. However, my target subject has been processed in Caret, so I do not have all the surface files for the target subject. To get rawfunc2surf-sess to work for my situation, I have to make some minor changes in its code. By looking at the code, I realized that rawfunc2surf-sess calls mri_vol2surf for mask and raw data, then it calls mris_fwhm to smooth raw data within mask. I am describing the changes that I have to make in these two commands, plus a specific question for each change: 1) mri_vol2surf includes the --cortex flag. Since I do not have cortex.label in the target subject, I am removing this flag. Would this be problematic later on? I will eventually do specific analyses on the occipito-temporal vertices in Matlab. Since I have lobar labels in the target subject, I can select/mask those vertices later on. 2) For the source subject, I have the white and pial surfaces. For the target subject, I have the midthickness surface which is somewhere between white and pial. I am adding --surf midthickness in mri_vol2surf to specify the target surface to be midthickness (instead of white). Will this be a problem when the source subject does not have such surface? 3) There is --projfrac 0.5 in mri_vol2surf. The help says "When [the projfrac is] set at 0.5 with the white surface, this should sample in the middle of the cortical surface. This requires that a ?h.thickness file exist for the source subject". I have the thickness file in the source subject - though I don't have it in the target subject. Does 'projfracing' happen only for the source subject? 4) I assume that mris_fwhm will work fine for my situation, unless it requires the white surface in the target subject. Which file is used in mris_fwhm for extracting the vertices coordinates? Thanks in advance for your advice, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
One more question: I tried to run: rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg iter05.sphere.reg -fwhm 2 -per-session And I got this: ERROR: experts key needed (-expkey) Not sure what this flag is. Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
Hi Doug, Removing -i fmc did not help, and I still get the same error. By looking at the rawfunc2surf-sess script, it looks like specifying an argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something for -expkey? Is this something that is used only in the name of log file? Thanks, Reza Try it without -i fmc On 10/08/2014 04:38 AM, Reza Rajimehr wrote: > One more question: > > I tried to run: > > rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg > iter05.sphere.reg -fwhm 2 -per-session > > And I got this: > > ERROR: experts key needed (-expkey) > > Not sure what this flag is. > > Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
Thanks Doug! I got it to work. The outputs are like fmc.sm2.F99.lh.iter05.nii.gz Should I still specify stem as fmc.iter05 in mkanalysis-sess? Reza Try added something like "-expkey iter05". When you make the analysis you will have to spec "-stem fmc.iter05" doug On 10/09/2014 12:12 AM, Reza Rajimehr wrote: > Hi Doug, > > Removing -i fmc did not help, and I still get the same error. > > By looking at the rawfunc2surf-sess script, it looks like specifying an > argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something > for -expkey? Is this something that is used only in the name of log file? > > Thanks, > Reza > > > Try it without -i fmc > > > On 10/08/2014 04:38 AM, Reza Rajimehr wrote: >> One more question: >> >> I tried to run: >> >> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg >> iter05.sphere.reg -fwhm 2 -per-session >> >> And I got this: >> >> ERROR: experts key needed (-expkey) >> >> Not sure what this flag is. >> >> Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Sulc maps
External Email - Use Caution Hi, In the .sulc files, the range of sulcal depth values are very different (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is there just a simple scaling factor here, or the procedure for calculating sulcal depth has been changed? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Sulc maps
External Email - Use Caution Thanks Doug! It would be great to know what the exact scaling factor is. The HCP data have been processed/analyzed using FS5.3. We have a set of new subjects that have been processed using the new version of HCP pipeline which is based on FS6.0. Since we want to compare the maps between the two datasets, we really need to know how the units are converted between the two versions of Freesurfer. Thanks in advance for your help, Reza I think it is probably just scaling, but it has been a long time since 5.3 and 6.0 On Mon, Nov 9, 2020 at 3:10 PM Reza Rajimehr wrote: > Hi, > > In the .sulc files, the range of sulcal depth values are very different > (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is > there just a simple scaling factor here, or the procedure for calculating > sulcal depth has been changed? > > Thanks, > Reza > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Sulc maps
External Email - Use Caution I should have mentioned that the HCP data have been processed using FS5.3HCP. If we know which code/script generates sulc files, we can try to dig out the code to find the scaling factor. On Thu, Nov 12, 2020 at 9:46 PM Reza Rajimehr wrote: > Thanks Doug! It would be great to know what the exact scaling factor is. > The HCP data have been processed/analyzed using FS5.3. We have a set of new > subjects that have been processed using the new version of HCP pipeline > which is based on FS6.0. Since we want to compare the maps between the two > datasets, we really need to know how the units are converted between the > two versions of Freesurfer. > > Thanks in advance for your help, > Reza > > > I think it is probably just scaling, but it has been a long time since 5.3 > and 6.0 > > On Mon, Nov 9, 2020 at 3:10 PM Reza Rajimehr wrote: > >> Hi, >> >> In the .sulc files, the range of sulcal depth values are very different >> (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is >> there just a simple scaling factor here, or the procedure for calculating >> sulcal depth has been changed? >> >> Thanks, >> Reza >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing group analysis results in tkmedit (3D) whileusing spherical space intersubject morphing
This is Doug's response to my question. It might be also relevant to your question. Reza ** Not directly. tkmedit is a volume viewer, and the spherical maps are of course on the surface. You can take your .w files and stuff them back into the volume with mri_surf2vol. doug Reza Rajimehr wrote: > Hi, > > Is there any way to visualize spherically-averaged maps in tkmedit-sess? > Currently, it seems that tkmedit-sess only accepts -space native or tal. > > Thanks, > Reza ** > Hi FreeSurfers, > > A small group analysis question of fMRI data (fixed effects). The target > brain is "fsaverage". > > I have resampled and averaged the stat maps across subjects in _spherical_ > space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / > stxgrinder-sess. Viewing the results on a "fsaverage" surface with > tksurfer works fine, thanks. > > Now I would like to also view the mean functional maps in 3D space > (tkmedit) on the "fsaverage" brain. This does not seem to work - obviously > because the results were calculated in spherical space and were never > resampled back to 3D space. > > Is there a way to resample the group average from sperical space to 3D > space so that it could be viewed in tkmedit? Or is the only way to achieve > something like this to recalculate the analyses entirely in Talairach > space without using the spherical space? > > To make the results actually comparable between 3D (tkmedit) and > surface-based (tksurfer) viewing, I think I should use the same type of > space for intersubject averaging - preferably spherical in both cases. > > Hence, if a tool such as sph2func-sess exists (could not find it in the > wiki), or there is a workaround, any suggestions would be very much > welcome. > > Thanks, > > Tommi > > --- > Tommi Raij, M.D., Ph.D. > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > Bldg 149, 13th St > Charlestown, MA 02129 > U.S.A. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Scale Bar
Hi, Does anybody have any idea what the scale bar shows in Tksurfer? I have heard that the scalebar is 10mm for the human brain. I am working with the monkey brain. Is the length of the scale bar 1cm for the monkey brain as well? Thanks, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scale Bar
Hi Bruce, Thanks for your email. Just to make sure: the original voxel size is 0.35 um isotropic. so in my case, the scale bar would be 3.5 mm, right? Thanks, Reza > it should be, unless you've "fooled" mri_convert into thinking the voxel > dimensions are different than what they are, which is a standard trick > with the monkey data. In that case its 10 of whatever your original voxel > dimensions were. > > cheers, > Bruce > > On Wed, 28 Jun 2006, Reza Rajimehr wrote: > >> Hi, >> >> Does anybody have any idea what the scale bar shows in Tksurfer? I have >> heard that the scalebar is 10mm for the human brain. I am working with >> the >> monkey brain. Is the length of the scale bar 1cm for the monkey brain as >> well? >> >> Thanks, >> Reza >> >> >> Reza Rajimehr, MD >> >> NMR Athinoula A. Martinos Center >> Department of Radiology >> Massachusetts General Hospital (MGH) >> Building 149, 13th St. >> Charlestown, MA 02129 >> >> Email: [EMAIL PROTECTED] >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A Possible Bug in Making Labels in Tksurfer
Hi (Doug, Kevin, ...), I am experiencing a problem with making labels in Tksurfer (for doing a subsequent ROI analysis). I did something as follows: 1) I loaded a functional activity map by surf-sess (human cortex). 2) Then, I loaded the full flattened cortical surface. 3) After right-clicking in the Tksurfer window, I clicked (left-clicking) on the center of 4 spatially distinct activity patches (i.e. 4 yellow spots of activity, which had no overlap with each other and no overlap with other yellow or blue patches). So 4 vertices were selected (as I saw in the command-line window). 4) Then, I openned the "Custom Fill" dialog box, and selected the following options: Fill Conditions: Up to and including paths, Up to functional values below threshold Fill From: All marked vertices Action: Create a new label After clicking the "Fill" button (in the "Custom Fill" dialog box) and then clicking the "Mark Label" button (in the Tksurfer window), the 4 patches were appropriately selected as white labels. In the command-line window: % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled surfer: filling (ctrl-c to cancel)... done, 542 vertices filled surfer: filling (ctrl-c to cancel). done, 105 vertices filled surfer: filling (ctrl-c to cancel). done, 954 vertices filled 5) I saved the selected label. In the command-line window: writing 2913 labeled vertices to /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. The problem is that the number of saved vertices is much more than the sum of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have this problem when I click on just 2 patches (rather than 4), and the number of saved vertices is the sum of vertices in the 2 patches. I also had this problem before, and I am worried that some additional vertices (voxels) are saved out of my control, which might affect the ROI analysis. Thanks for any help, Best, Reza **** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] A Possible Bug in Making Labels in Tksurfer
Hi Kevin, on machine monkeylove source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects cd /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/Human_Eccen/Katie/MYSTUDY surf-sess -sf sf.txt -df df.txt -analysis Analysis_Human_Eccen -contrast 123456 -map sig -hemi rh I changed the min threshold to 4 (linear) in the Tksurfer window (view - config overlay ...). Reza > Thanks for this report. Can you point me at the data you were using, > whether you were using the std or dev environment, and what command > you used to start tksurfer? > > On Tue, Dec 12, 2006 at 11:28:45PM -0500, Reza Rajimehr wrote: >> Hi (Doug, Kevin, ...), >> >> I am experiencing a problem with making labels in Tksurfer (for doing a >> subsequent ROI analysis). I did something as follows: >> >> 1) I loaded a functional activity map by surf-sess (human cortex). >> >> 2) Then, I loaded the full flattened cortical surface. >> >> 3) After right-clicking in the Tksurfer window, I clicked >> (left-clicking) >> on the center of 4 spatially distinct activity patches (i.e. 4 yellow >> spots of activity, which had no overlap with each other and no overlap >> with other yellow or blue patches). So 4 vertices were selected (as I >> saw >> in the command-line window). >> >> 4) Then, I openned the "Custom Fill" dialog box, and selected the >> following options: >> >> Fill Conditions: Up to and including paths, Up to functional values >> below >> threshold >> >> Fill From: All marked vertices >> >> Action: Create a new label >> >> After clicking the "Fill" button (in the "Custom Fill" dialog box) and >> then clicking the "Mark Label" button (in the Tksurfer window), the 4 >> patches were appropriately selected as white labels. In the command-line >> window: >> >> % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled >> surfer: filling (ctrl-c to cancel)... done, 542 vertices filled >> surfer: filling (ctrl-c to cancel). done, 105 vertices filled >> surfer: filling (ctrl-c to cancel). done, 954 vertices filled >> >> 5) I saved the selected label. In the command-line window: >> >> writing 2913 labeled vertices to >> /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. >> >> >> The problem is that the number of saved vertices is much more than the >> sum >> of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have >> this problem when I click on just 2 patches (rather than 4), and the >> number of saved vertices is the sum of vertices in the 2 patches. I also >> had this problem before, and I am worried that some additional vertices >> (voxels) are saved out of my control, which might affect the ROI >> analysis. >> >> Thanks for any help, >> >> Best, >> Reza >> >> >> Reza Rajimehr, MD >> >> NMR Athinoula A. Martinos Center >> Department of Radiology >> Massachusetts General Hospital (MGH) >> Building 149, 13th St. >> Charlestown, MA 02129 >> >> Email: [EMAIL PROTECTED] >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Kevin Teich Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer window too small
Just zoom out the image in the Tksurfer window. There are zoom in and zoom out buttons in the Tksurfer menu. Reza > Hi all, > > When I displayed a flattened image of the entire cortex > (lh.full.patch.flat) > on the tksurfer window, > the image was too big for the tksurfer window, meaning the falttened image > is chopped out. > > Is there any way that I can display the entire flattened image on the > tksurfer window? > > Thanks. > > Nam. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] omnibus contrast / paint-sess
Hi Sheeva, With stxgrinder-sess, t-test is not saved when contrast is "omnibus", probably because omnibus contrast is "all tasks vs. fixation" and t-test would be irrelevant. Reza > Hello, > > I am trying to create and view an omnibus contrast for one subject. When > I type the appropriate command: > > paint-sess -analysis SNgamma -contrast omnibus -space sph -spacedir > sphsm20 -d . -s sub28a -subject sub28_recon > > I get the following error: > - > paint-sess logfile is > /autofs/space/perun_004/users/sheeva/fMRIanal/log/paint-sess.log > - > setenv SUBJECTS_DIR /space/perun/3/users/cylix/Subjects > INFO: painting onto white > grep: /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/session.info: > No such file or directory > SpaceDiris sphsm20 > SpaceSubDir is sphsm20 > INFO: setting srcsubject to ico > -- lh hemisphere -- > Thu Mar 8 13:12:00 EST 2007 > SpaceDir is sphsm20 > INFO: Painting onto sub28_recon > ERROR: cannot find any files with > /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/bold_SN/SNgamma/sphsm20/omnibus/sig-lh > > It seems that stxgrinder-sess created fsig, f, iminsig, and minsig files, > but did not create t or sig files. This only occurred for the omnibus -- > it didn't happen with the other contrasts. I don't know if I should be > doing something differently for the omnibus as compared to the other > contrasts -- any insight would be greatly appreciated. > > Thank you! > Sheeva Azma > > FREESURFER_HOME: /usr/local/freesurfer/stable > Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070308 > RedHat release: CentOS release 4.4 (Final) > Kernel info: Linux 2.6.9-42.0.3.ELsmp i686 > NMR Center info (/space/freesurfer exists): > machine: perun > SUBJECTS_DIR: /space/perun/3/users/cylix/Subjects > PWD: /autofs/space/perun_004/users/sheeva/fMRIanal > > > > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] skull strip for monkeys
Hi Paul, Make smart cuts to simplify the normalization and skullstrip steps. This is done using tkmedit --> tkmedit monkey orig to open the volume, and then selecting --> Tools > Volume > Smartcut after positioning the cursor (red cross) at the desired location. Smart cuts are only orthogonal and calculated as follow: if the cursor is in the upper half of the volume, everything above the cursor will be removed; if the cursor is in the right half of the volume, everything to the right will be removed, etc. It is not necessary to strip all the skull (and may not be necessary to strip any of the skull); the point is only to disrupt the skull to make the strip process more effective. Reza > Hello All, > > I am having a very difficult time getting skullstrip to work on my monkey > anatomical data set. Are there any suggestions on how to get it to work > properly? > > Thanks in advance > > Paul > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] read_curv
Hi, Using "read_curv", I load the curvature file into Matlab. How can I get the corresponding vertex indices for these curvature values? Thanks, Reza **** Reza Rajimehr, MD Postdoctoral Research Fellow NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th Street Charlestown, MA 02129 Phone: 617-669-0930 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ces and percent signal change
Hi, For a stimulus condition 'A' and a fixation condition, does the ces file for the contrast 'A - fix' correspond to the % signal change for the condition A? Thanks, Reza **** Reza Rajimehr, MD Postdoctoral Research Fellow NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th Street Charlestown, MA 02129 Phone: 617-669-0930 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] run-recon-monkey
Hi, I have a question regarding convertion of raw multi-echo data to bfloat format. I used the following command in seychelles: pbsubmit -c "run-recon-monkey /space/stego/5/users/wim/edgar050218 1 6 7 8 > edgar050218_1.out" -p -m [EMAIL PROTECTED] The converstion has been done succesfully for one functional run but then it has been stoped and there is the following error message: ??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_adc_VA21.m On line 114 ==> adc_data = reshape(adc_data, 2, mdh.SamplesInScan); Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_adc.m On line 5 ==> [adc_data, mdh] = read_mdh_adc_VA21(fid); Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_and_mrprot.m On line 151 ==> [adc_data, mdh] = read_mdh_adc(fid,VersionNum); Error in ==> /homes/4/greve/anders/recon_Monkey_fMRI.m On line 199 ==> [kdat1,krev1,ktim1,pcdat1,pcrev1,pctim1,h1] = .. . I do not know what this error message refers to. I would be thankful if anyone has a suggestion. Best Wishes, Reza -- **** Reza Rajimehr, M.D. NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] autoreg-sess and spmregister-sess problem
Hi, In the FS-FAST analysis stream (dev environment), I used autoreg-sess command as follows: autoreg-sess -s mvp022106 -df df.txt It successfully generated a register.dat file in the bold directory. Then I used tkregister-sess as follows: tkregister-sess -s mvp022106 -df df.txt -rsd t1epi When tkregsiter window comes, the structural volume (anatomical T1) is OK but t1epi volume is completely corrupted. However, running tkregister-sess with '-rsd t1epi' generates another register.dat file in the directory above the bold directory. When I use this register.dat file in the tkregister-sess command, t1epi volume looks fine and almost in the appropriate location as T1 volume. I also tried spmregister-sess instead of autoreg-sess: spmregister-sess -s mvp022106 -df df.txt -fsd bold A register.dat file is generated by this command in the bold directory. Then I used tkregister-sess as follows: tkregsiter-sess -s mvp022106 -df df.txt -fsd bold In the tkregsiter window, the functional volume looks fine but it is largely displaced. I could finally register it manually. I might do something wrong with autoreg-sess and spmregister-sess or is there a bug for these commands? Thanks, Reza **** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] problem in curv surface
Hi, I have recently reconstructed a brain using "recon-all -autorecon" in dev environment. First I converted anatomicals to mgz format and then I ran the following commands sequentially: recon-all -subjid subject -autorecon1 -legacy recon-all -subjid subject -autorecon2 The reconstruction has been done successfully without error. The inflated surface is almost fine (without topological defects) but the "curv" surfaces (curv.lh and curv.rh) do not look normal. They have only red boundaries (sulci); the green boundaries (gyri) are absent. The sulc surfaces look fine though. on machine monkeylove source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/ship/3/users/reza/mvp022106/3danat which recon-all /usr/local/freesurfer/dev/bin//recon-all cd /space/ship/3/users/reza/mvp022106/MYSTUDY Thanks for any comments, Reza **** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
