[Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

Hi dear all, I'm new here and I've a simple question that how could I transfer the reconstructed pial surface file(like lh.pial) into a 256*256*256 matlab matrix used in later fast marching process? Any suggestion will be appreciated! Thank guys. Best, Yunxin Wang

[Freesurfer] Mapping data into segmented atlas

Hi Freesurfers, I had run Freesurfer over a set of MRIs, extracted the volumes for different ROIs and correlated with another biomarkers using R. Now I want to represent the obtained correlations for the segmented ROIs into a brain template. Is there some automated way to do that with

Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

Hi Yunxin the surface lives in a continuum and is 2D. Do you mean filling the space between the ?h.white and ?h.pial surfaces? We do that as part of recon-all and create ribbon volumes in the mri dir cheers Bruce On Mon, 5 Aug 2013, Yunxin Wang wrote: Hi dear all, I'm new here and I've a

[Freesurfer] Controlling for shape (and size) of a ROI in co-registration

Hi FS Community, Is there a way to control for the size and shape of a ROI when applying co-registration? For instance, I drew a ROI in a scan through freesurfer, and then when I coregistered that ROI to another scan, the resulting ROI had a different shape and number of voxels compared to the

Re: [Freesurfer] Trac-all question

Hi Alan - On the tutorial page you need to follow the directions under If you are not at an organized course, and $TUTORIAL_DATA is whatever directory you have downloaded the tutorial data in. Please address questions to the list and not to me personally, as other people may have the same

Re: [Freesurfer] Controlling for shape (and size) of a ROI in co-registration

Hi Panos, not unless you want to restrict the registration to be rigid (6 dofs) cheers Bruce On Mon, 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, Is there a way to control for the size and shape of a ROI when applying co-registration? For instance, I drew a ROI in a

[Freesurfer] Fwd: TR,TE,TI,FA variability w/ mri_ca_train

-- Forwarded message -- From: Mark Plantz markplantz2...@u.northwestern.edu Date: Mon, Aug 5, 2013 at 11:32 AM Subject: Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train To: Bruce Fischl fis...@nmr.mgh.harvard.edu thank you. Would the command simply be something like this:

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

For some reason, when I run that command, I get the following output: Input volume is : seg_mov Output volume is : seg_mov_2 There are no errors, but when I check mri_info of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen? Thanks! MP

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

can you send us the full command line and screen output of what you ran? On Mon, 5 Aug 2013, Mark Plantz wrote: For some reason, when I run that command, I get the following output: Input volume  is : seg_mov Output volume is : seg_mov_2 There are no errors, but when I check mri_info of the

[Freesurfer] wmparc.stats

Dear FreeSurfer Experts, I'm looking at stats/wmparc.stats, and there are some inconsistencies between subjects. I am wondering what might be the cause. For one subject (say subject 1), part of the information appears to be: # NRows 66 # NTableCols 10 # ColHeaders Index SegId NVoxels

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

Command and output: dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0 seg.mgz seg_new.mgz Input volume is : seg.mgz Output volume is : seg_new.mgz dhcp-165-124-23-213:Desktop IngvalsonLab$ Then, I checked the mri_info for each of the files (input and output) -

[Freesurfer] Monte Carlo

Good afternoon, I am getting much different results in my QDEC before and after running monte carlo cluster correction. Upon initially running the QDEC I have what appears to be a significant group difference in the prefrontal region that does not show up after I run the Monte Carlo but at the

[Freesurfer] hemispheric masks?

Dear freesurfer experts, I was wondering whether there is an existing mask for the left and right hemispheres for fsaverage. I can't seem to find any documentation of this, but perhaps I am missing something? Thanks in advance, John. ___

Re: [Freesurfer] hemispheric masks?

It is stored as a label, see fsaverage/label/?h.cortex.label doug On 8/5/13 1:14 PM, John Richey wrote: Dear freesurfer experts, I was wondering whether there is an existing mask for the left and right hemispheres for fsaverage. I can't seem to find any documentation of this, but perhaps I

[Freesurfer] trac-preproc

Hi All: When I ran trac-preproc I got an error that read s as follows: trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have a bvec.txt and bval file in each directory. thanks for your help, Alan The following are the messages:

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

Oh, I see. It checks against zero to see if things are specified. I'll fix that, but in the meantime why don't yo uset everything to 1 instead of 0 On Mon, 5 Aug 2013, Mark Plantz wrote: Command and output: dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0 seg.mgz

Re: [Freesurfer] trac-preproc

The error says: `/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt': No such file or directory Does this file exist? On Mon, 5 Aug 2013, Alan Francis wrote: Hi All: When I ran trac-preproc I got an error that read s as follows: trac-preproc exited

Re: [Freesurfer] long_mris_slopes sign of do-rate

Hi Vincent, yes, it is tp2-tp1 / time_delta so thinning is negative, thickening positive. I'll correct the help text, the tutorial is right. It knows about the time point ordering because of the time column. Best, Martin On 08/02/2013 09:04 PM, vbrun...@nmr.mgh.harvard.edu wrote: Dear

Re: [Freesurfer] trac-preproc

Hi Anastasia: Yes this file does exist but it did not have the *.txt suffix. Maybe I will change the suffix and run this again. thanks, Alan On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The error says:

Re: [Freesurfer] longitudinal stream percentage change

Hi Bastian, actually (see other mail today) it computes percent thickening per year as it is the slope of the linear fit into the measurements (thickness with respect to age or time). If the slope is negative, there is thinning. The results (within subject and on fsaverage) have signs so they

Re: [Freesurfer] longitudinal stream percentage change

By the way, smoothing can remove the thickening (if there is only a little and mainly thinning ). Best, Martin On 08/05/2013 02:18 PM, Martin Reuter wrote: Hi Bastian, actually (see other mail today) it computes percent thickening per year as it is the slope of the linear fit into the

Re: [Freesurfer] Best way to generate Complete Stats Table

Dear Doug and Bruce, Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well? Best wishes, Sal On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: try asegstats2table

Re: [Freesurfer] trac-preproc

Hi Alan - The file doesn't need to have an extension, .txt or other. But you do need to set bvecfile to the full name of the file, including the extension, if it has one. a.y On Mon, 5 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes this file does exist but it did not have the *.txt

[Freesurfer] tksurfer and mountain lion problem / question

Hi, I can run freeview using my current install on Mountain Lion, however when I run tkmedit or tksurfer I get the following error: GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0 my /etc/profile has the setting export DISPLAY=:0.0 for a different program. Is there settings I

Re: [Freesurfer] Controlling for shape (and size) of a ROI in co-registration

I see, thanks Bruce! Hi Panos, not unless you want to restrict the registration to be rigid (6 dofs) cheers Bruce On Mon, 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, Is there a way to control for the size and shape of a ROI when applying co-registration? For

Re: [Freesurfer] Best way to generate Complete Stats Table

Good question:). It does not look like we are currently creating a stats file for the subfields, which means you will have to do it yourself. You can do it with something like cd $SUBJECTS_DIR/subject mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv mri/norm.mgz

Re: [Freesurfer] Best way to generate Complete Stats Table

Thank you! -Sal On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Good question:). It does not look like we are currently creating a stats file for the subfields, which means you will have to do it yourself. You can do it with something like cd

[Freesurfer] Error with recon-all: You are trying to re-run an existing subject

Hi All, I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid SPAR_016_130708), I get this error message: ERROR: You are trying to re-run an existing subject with (possibly) new input

Re: [Freesurfer] wmparc.stats

That is a little strange. Can you look at the wmparc.mgz to see if it is there? Also look at the aparc+aseg.mgz to see how big the cortical region for caudalanteriorcingulate is. The wmparc is based on the aparc part of aparc+aseg. doug On 8/5/13 12:49 PM, Yang, Daniel wrote: Dear

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject

Hi Joe try adding -all to the end. You need to specify a directive for it to carry out cheers Bruce On Mon, 5 Aug 2013, Joseph Andreano wrote: Hi All, I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i

Re: [Freesurfer] Monte Carlo

Something is going wrong. Can you carefully document the key strokes and mouse clicks you used? doug On 8/5/13 1:08 PM, Peter Boulos wrote: Good afternoon, I am getting much different results in my QDEC before and after running monte carlo cluster correction. Upon initially running the

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject

are you looking in the right place? Look in $SUBJECTS_DIR, not the current directory doug On 8/5/13 5:45 PM, Joseph Andreano wrote: Hi All, I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i

Re: [Freesurfer] Mapping data into segmented atlas

There is not an automated tool. I would do it in matlab, loading in the segmentation, for each seg find the voxels in the segmentation and set their values equal to your computed value. You can use MRIread.m and MRIwrite.m doug On 8/5/13 6:37 AM, Oscar Sotolongo Grau wrote: Mapping data

[Freesurfer] Group thickness means

Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by

Re: [Freesurfer] tksurfer and mountain lion problem / question

Hello Sal, I tried setting my display to :0.0 and was able to get the tkmedit program to open on my Mac Mountain Lion machine so Im not exactly sure why yours is having difficulty. Have you installed XQuartz? http://xquartz.macosforge.org/landing/ If you already have XQuartz installed I would

[Freesurfer] Binary mask

Hi FS Community, Is there a way to create a binary mask of everything that is inside the cortical ribbon of a subject (including the cortical ribbon)? I ran: mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me a binary mask of the cerebral cortex, but I was wondering whether

Re: [Freesurfer] Group thickness means

You should setup contrasts to test the group mean for each group separately in addition to your contrast of interest. I'm actually not sure whether QDEC will do this for you or not. Then cd glmdir/group1contrast mri_segstats --annot fsaverage lh

Re: [Freesurfer] Binary mask

by everything inside you mean subcortical white matter and gray matter? If so, look at ribbon.mgz doug On 8/5/13 6:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, Is there a way to create a binary mask of everything that is inside the cortical ribbon of a subject (including the

Re: [Freesurfer] dPSD and ev duration

Hi Ella, sorry for the delay. The VRF gets reduced by a factor roughly equal to TR/dPSD, so 5 in your case. Whether this matters depends on how you eventually want to analyze the data. If you are going to assume a shape to the HRF (eg, using SPM or FSL), then it won't make much difference

[Freesurfer] Group thickness means

Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by

Re: [Freesurfer] function that do the same step like qcache?

The argument to --src_type should be the input file (eg, lh.curv, lh.sulc, lh.thickness). The --trgsurfval should be the name of the output file and --trg_type should be curv doug On 7/30/13 3:25 AM, fatma zribi wrote: Dear Bruce, I try to execute this command to smooth and resample data

Re: [Freesurfer] funcroi-table-sess error

Hi Alex, are you running it from the project folder? It is looking for a folder called log in the current directory. It should be creating this folder (bug). So, if you run it from the project folder, the log folder will be there. Or can create a log folder in your current directory (mkdir

[Freesurfer] functional ROI-based structural statistics?

Dear FreeSurfer Experts, Theoretically, if you have a set of functional ROIs, is it possible to derive the cortical thickness, white surface area, and gray matter volume of those functional ROIs in FreeSurfer? Many thanks!! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale

Re: [Freesurfer] wmparc.stats

I check the recon-all.log. It appears that the cortical region for caudalanteriorcongulate for this subject is very small.. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm)