[Freesurfer] Flipping Surface .mgh file to opposite hemisphere via fsav_sym

Dear Freesurfer-Experts, I am trying to flip surface files (.mgh) from right to left. I have read your instructions concerning xhemi and performed registration to fsaverage_sym: foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym -

[Freesurfer] Different significant clusters: qdec vs mri_glmfit-sim

Hi Freesurfer experts, Qdec does not appear to allow me to automatically extract mean values for significant clusters for each participant, so I have been doing this using command line after running the original analysis in Qdec. However, I have found that there are some differences in the signifi

[Freesurfer] FSFAST (seed based correlation analysis)

Hi Freesurfers, How can I perform seed based correlation analysis using PET images? In other words how can I use the same approach of FSFAST, but by including PET images instead of fmri images, to study the correlation between PET signal within a seed mask ( e.g precentral gyrus ) and the whole

Re: [Freesurfer] missing baseline in longitudinal analysis

Just leave out that row (second case) Best Martin On Apr 13, 2016 8:30 AM, Mihaela Stefan wrote:Hi Martin! Sorry to bug you but I have one more question. How do I create the Qdec table without the baseline for that subject? Do I leave the baseline time point out or I still enter it in the table?

Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

Thanks, Doug. When I do it, I get the following error: ERROR: must spec --sim I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that mri_mcsim got an atualization for Linux. Should I get that atualization for Mac Os? Best, Pedro. On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve wrote: > T

Re: [Freesurfer] Freesurfer v6 beta

Hi again, in the paper, we used FreeSurfer 5.3 the process the data (recon-all), and then run the hippocampal module on top of that. So, with a bit of trouble, you can reproduce the results.. However, the 6.0 beta was taken down, so reproducing the results of the recon-all stream would be hard

Re: [Freesurfer] Freesurfer v6 beta

Hi Eugenio, I understood this part that you mentioned but I didn't understand how is is affected and what would be its consequences? Because I am referring to your preprint paper that makes use of v6, so will the results/validity of that paper also get affected by these differences. Because in my

Re: [Freesurfer] Freesurfer v6 beta

Hi Tyson, the hippocampal module shouldn't change between your beta and the FS6 release, but the main recon-all stream will. Since the latter is used to initialize the former, the results will be a bit different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeigl

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

what is your tksurfer command line? Can you send all the terminal output from tksurfer? Does it work in freeview? On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote: > Hi, > > I’m trying to take an ROI in MNI152 volume space and make it into a > cortical surface label, for visualization purpose

Re: [Freesurfer] mri_vol2surf after recon-all

this is a known bug. Try this version instead ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote: > Hi Doug > > So I tried running mni152reg and had the following error: > > mni152reg --s icbm-102_test > > > setenv SUBJECTS_D

Re: [Freesurfer] missing baseline in longitudinal analysis

Hi Martin, I am reposting this. Should we include the missing baseline in the qdec table or leave it out? Thanks! Mihaela On Wed, Apr 13, 2016 at 8:30 AM, Mihaela Stefan wrote: > Hi Martin! > Sorry to bug you but I have one more question. How do I create the Qdec > table without the baseline f

Re: [Freesurfer] Oblique Slice Acquisition

Just an aside: if you acquire oblique (e.g. AC/PC aligned), and don’t want FS to rotate the volume back into the native scanner space as part of its “conformation” step, you can edit the s/qform of the NIFTI header to appear as a non-oblique acquisition. As Bruce noted, this isn’t a big deal, alth

[Freesurfer] Open Research Assistant position at the VA

Hi FreeSurfers, There is a research assistant position opening at the VA Boston Healthcare System in neuroimaging and aging (job announcement is attached). This would be a great position for someone who is interested in both the technical aspects of MRI data processing/analysis as well as in neuro

[Freesurfer] Freesurfer v6 beta

Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson ___ Freesurfer mailing list

Re: [Freesurfer] .license and tksurfer

Do you have a .license file in your /Applications/freesurfer directory? If so try making a copy of it and calling it license.txt and try again. If that still doesnt work please email me your .license file TO MY PERSONAL EMAIL ADDRESS, NOT THE FREESURFER LIST. Thanks. -Zeke On 04/13/2016 01:38

[Freesurfer] .license and tksurfer

Hi list, please see the error reported below. It occurs when I invoke tksurfer.Of note, I have completed without problem fs-fast analysis without error.The .license file is well placed and written.Thanks Stefano tksurfer fsaverage rh inflated -aparc -overlay subj/rest/fc.ROI.surf.rh/ROI/sig.nii.

Re: [Freesurfer] Oblique Slice Acquisition

Hi Kate I don't think that will matter. Try running it through from the original dicoms and see if things seem accurate. That isn't actually an artifact, it just looks strange because of the slight angle of the view. My guess is we will handle this fine cheers Bruce On Wed, 13 Apr 2016, Ka

Re: [Freesurfer] mri_vol2surf after recon-all

Hi Doug So I tried running mni152reg and had the following error: mni152reg --s icbm-102_test setenv SUBJECTS_DIR /data-01/trisanna/freesurfer cd /home/trisanna /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test fslregister --mov /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.ni

[Freesurfer] DLPFC seed

Hi all, I'm trying to do FC connectivity analysis using the dorsalateral prefrontal cortex as a seed. I checked the text file $FREESURFER_HOME/average/colortable_desikan_killiany.txt and it looks like DLPFC is not listed as a possible structure to do the FC analysis. I attempted to use lh-prefr

Re: [Freesurfer] TRACULA

I could be wrong, but the output in your email oscillates between "/Users" and "Users" (Note the preceding forward slash). Im not sure if thats just a copy/paste thing or directly related to your error. -Zeke On 04/12/2016 08:44 PM, Jasmin Alves wrote: > > > So I have specified where the DTI fi

[Freesurfer] Summer School "Advanced Scientific Programming in Python" in Reading, UK, September 5--11, 2016

*Advanced Scientific Programming in Python* a Summer School by the G-Node, and the Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading, UK Scientists spend more and more time writing, maintaining, and debugging software

[Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

Hi, I’m trying to take an ROI in MNI152 volume space and make it into a cortical surface label, for visualization purposes. With my input being the lh thresholded, binarized MNI152 nii.gz label (when I visualize it, it looks as it should in fslview), I ran: mri_vol2vol -- mov -- targ $SUBJE

Re: [Freesurfer] mri_surfcluster issues

Dear Doug, thank you very much for the support. I am quite confused by this info about correcting of area of fsaverage clusters. Could you please clarify to me the following: How exactly the values of lh.area, lh.white.avg.area.mgh of fsaverage were computed? How the cluster area inside mri_s

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

Thank you! - Ursprüngliche Mail - Von: "Douglas Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 13. April 2016 16:46:19 Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC In most neuroimaging, people use p<.01 (sig threshold > 2). It is more important to have

Re: [Freesurfer] correcting mri_glmfit results

Looks like you are analyzing a table of data (ie, ROI analysis). In this case you cannot use clusterwise correction because you cannot form clusters of voxels when you don't have a voxel-wise analysis! You can do a bonferroni or FDR correction. You can get an FDR program from here ftp://surfer

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

In most neuroimaging, people use p<.01 (sig threshold > 2). It is more important to have a more stringent threshold when using gaussian random fields because the assumptions built into it. Since we use simulations directly, we don't have problems with those assumptions and so I think you can go

Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

Try it without the --no-sim. The --no-sim was from before I stored the cached data and you either had to run a simulation or not. On 4/12/16 9:10 PM, Pedro Rosa wrote: Dear list, I want to limit my vertex-wise group analysis to a smaller spatial region, then I ran my own Monte-Carlo simulation

Re: [Freesurfer] correcting mri_glmfit results

Hi Clara, You need to register and smooth again for only the first time point. You could also open the full stack in Matlab, select the entries of your first time point and write it out again. Best Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] PET voxelwise

Hi Doug, One more question about feeding the -reg to mri_vol2surf, please. I am specifying the registration .lta because I have made edits to it, mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh --r

[Freesurfer] correcting mri_glmfit results

Dear FreeSurfer experts, I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/l

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

Hi Doug, thanks for your reply. It made things a lot clearer. I totally understand that you're probably receiving more than one cry for help per day. What would you say are the conventions for picking a threshold for analyses on structural data? Cheers, Clara - Ursprüngliche Mail -

Re: [Freesurfer] missing baseline in longitudinal analysis

Hi Martin! Sorry to bug you but I have one more question. How do I create the Qdec table without the baseline for that subject? Do I leave the baseline time point out or I still enter it in the table? For example fsid fsid-base years Study1_Subj1_MRI0. Study1

[Freesurfer] Repeated measures of one group analysis question

Dear FreeSurfer experts I have a question regarding the correct data analysis method for my study design and could unfortunately not find an example of a similar analysis on your mailing list or documentation on the wiki. I have repeated structural MRI data from one group (within-subjects design)

Re: [Freesurfer] TRACULA

Jasmin - Check the DTI.nii.gz file using MRICRON and see if the images across the gradients are OK. If the file is corrupt, then Tracula cannot read this. best, A On Tue, Apr 12, 2016 at 8:44 PM, Jasmin Alves wrote: > > > So I have specified where the DTI file is. I am not sure why Tracula >

[Freesurfer] Extract random effects for correlation

Dear FS experts,  I used the spatiotemporal LME to fit to my longitudinal data and performed some ad-hoc tests using the FDR2 correction.  May I know how can I extract the random slopes characterizing individual variability in rate of change of cortical thickness at the significant vertices,