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How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
by Knut J Bjuland 07 Dec '12

07 Dec '12

How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

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De-trending resting state data
by Chris McNorgan 06 Dec '12

06 Dec '12

I'm working with raw timeseries waveform data from a resting state dataset. There's one run per participant, so no between-run normalization is required. With Doug's help, I have mastered extracting the timeseries information from individual ROIs in surface space. The timeseries data is the product of the preproc-sess script, to which I additionally added the -inorm parameter to extract the mean timeseries for the entire volume. One concern I had was that correlations between timeseries from different ROIs might be artificially inflated by scanner drift. For example, if the overall signal increases or decreases as a function of time over the course of the run or fluctuates periodically, then for any two regions, their signals will go up or down together as a result. This should in turn make the timeseries from these two regions more correlated. I have no strong evidence that scanner drift is a particular problem in my dataset, but it seems likely enough in a 6 minute run that I want to mitigate the problem. I can't really put these data through selxavg, as I do not have a model to fit for resting state data, and in any case would like to work with the timeseries itself, rather than residuals or any other by-product of an HRF model. I was wondering if simply subtracting the global mean signal waveform from each ROI waveform would be a reasonable strategy for removing drift, or if there are any standalone commands that are called by some of the super-scripts that I can use without carrying out a first level analysis. Thanks, Chris

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update mri_glmfit
by Knut J Bjuland 06 Dec '12

06 Dec '12

Hi I saw an updated version of mri_glmfit in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86…. Should I update this file in my freesurfer installation. What do this fix? Is is not in the release notes? Knut J

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Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 06 Dec '12

06 Dec '12

The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat difficult for me to support the version 4 stream because it is so old. doug On 12/06/2012 03:27 PM, Julia Foecker wrote: > I have the two versions 4 and 5 , but I am receiving the same error > messages with 5.1 > For example when I type in preproc-see there is no -surface as well. > Isn't there any other possibility to solve that issue? > > It may have also sth. to do with the computer. I have a new Mac, not > sure if this may be the reason. > As I said, I do not think this is due to the version...I just tried > that and similar requirements are missing when I am doing that with 5.1 > > Thanks again for further advices, > Julia > > > > On 12/6/12 11:56 AM, Douglas N Greve wrote: >> Julia, what version of FS are you using? It looks like pre-5.0. Can >> you upgrade to 5.1? There were a lot of changes in going from 4 to 5, >> and it is becoming increasingly hard to support version 4. >> >> doug >> >> >> >> On 12/06/2012 02:45 AM, Julia Foecker wrote: >>> thanks. >>> attached the info file. >>> >>> When I run the surf-sess command after that, it shows the functional >>> on a >>> surface (see attached but the values at the occip regions show >>> "inf." (see >>> figure 1 attached). >>> Moreover, when I try to load the occipital patch it shows me the >>> attached file >>> (fig.3) and I cannot use the command -> configure -> overlay to change >>> settings. >>> >>> I have used fake ecc. runs (I have recorded only polar runs). >>> >>> Would you have any further suggestions? >>> Thanks, >>> Julia >>> >>> On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu> >>> wrote >>> >>>> It should automatically detect that this was a retinotopy analysis and >>>> then load the polar and eccen. Was this configured as a retinotopy >>>> analysis? Can you send me the >>>> >>>> $ANALYSIS_PHASE/analysis.info file? >>>> >>>> doug >>>> >>>> >>>> >>>> On 12/05/2012 04:12 PM, Julia Foecker wrote: >>>>> Hi Doug, >>>>> >>>>> I tried now several ways to get the maps on the surface: >>>>> >>>>> 1. When I am deleting -retinotopy flag and type in: >>>>> >>>>> >>>>>>> tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY >>>>>>> -analysis $ANALYSIS_PHASE >>>>> I got the message:no contrast has been specified >>>>> >>>>> (I do not have any contrasts in the analysis, just use polar angle >>>>> maps) >>>>> >>>>> >>>>> 2. I tried to use the commands on the website you referred to, but >>>>> I do not >>>>> have -surface in the preproc-sess (see attached) >>>>> The other commands depend on this preproc-sess command. >>>>> >>>>> >>>>> 3. I tried the following command >>>>> paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis >>>>> $ANALYSIS_PHASE >>>>> >>>>> >>>>> and I got the errors listed below... >>>>> >>>>> I am not sure how to procede. Would you have any further suggestions? >>>>> Many thanks, >>>>> Julia >>>>> >>>>> Thanks, >>>>> Julia >>>> >>>> >>>> >>>> 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. >>>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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how is fsnr computed?
by Alex Kell 06 Dec '12

06 Dec '12

freesurfers, i've been using my own scripts to compute tSNR for data i was running through FSL, but i'm now running the data through freesurfer and i wanted to better understand what the fsnr volumes spit out by selxavg3-sess are. i poked around the wiki and mailing archives and couldn't find answers to the following questions: 1. how is fsnr computed? tsnr is <mean_of_vox_time_course>/<std_of_vox_time_course> -- is fsnr the same thing with a different name? 2. what kind of preprocessing is done on the data before fsnr is computed? since freesurfer removes linear trends at the modeling stage, not the preprocessing stage, are linear trends removed from the data going into fsnr calculations? is anything else regressed out before fsnr is computed (e.g., other nuisance regressors)? 3. what's the difference between raw.fsnr.nii.gz, fsnr.nii.gz, and fsnr2.nii.gz? 4. is fsnr.dat the mean in the whole brain mask (i.e., gm and wm)? separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes? thanks in advance! alex kell

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image flip after use of mri_vol2surf/mri_surf2vol
by Fonteijn, H.M.J. (H.) 06 Dec '12

06 Dec '12

Hello, I'm relatively new to Freesurfer so chances are that this is a pretty basic error on my side but here goes anyhow. I'm trying to use mri_vol2surf for surface-based smoothing of functional MRI data. I would then like to extract time courses from the surface with spm functions by converting the surface to a volume again with mri_surf2vol. Specifically the commands I'm using are: bbregister --s subject0016 --mov volume0001.nii.gz --reg epi2T1.dat --init-spm --bold mri_vol2surf --mov volume0001.nii.gz --reg epi2T1.dat --surf-fwhm 8 --hemi lh --projdist-avg 0 1 0.1 --o ./volume0001Surf_lh.w --out_type paint mri_surf2vol --surfval volume0001Surf_lh.w paint --hemi lh --projfrac 0.5 --reg epi2T1.dat --o volume0001Surf2Vol_lh.nii --template volume0001.nii.gz Registration looks allright with tkregister2. I'm only using one volume (volume0001.nii.gz) to test this set of commands. However if I now view volume0001Surf2Vol_lh.nii in fslview, it shows the hemisphere on the right. I'm pretty sure that this is actually the left hemisphere but now flipped. I wonder how this can be solved. All the best, Hubert

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Running recon-all on a series of scans
by Natasha Jawa 06 Dec '12

06 Dec '12

Hi, Is it possible to run recon-all on a series of scans? I have multiple scans that I want to process longitudinally. The .nii files have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz, 002.mgz, etc.) in /Applications/freesurfer/subjects/<subjid>/mri. I've tried running recon-all on this whole folder with the command line: recon-all -subjid <subjid> -all, but it does not execute properly. Do I have to run each of these scans separately using recon-all (i.e., do I need to use a separate terminal for each scan)? Thank you in advance for your time and help.

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Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 06 Dec '12

06 Dec '12

Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: > thanks. > attached the info file. > > When I run the surf-sess command after that, it shows the functional on a > surface (see attached but the values at the occip regions show "inf." (see > figure 1 attached). > Moreover, when I try to load the occipital patch it shows me the attached file > (fig.3) and I cannot use the command -> configure -> overlay to change > settings. > > I have used fake ecc. runs (I have recorded only polar runs). > > Would you have any further suggestions? > Thanks, > Julia > > On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > wrote > >> It should automatically detect that this was a retinotopy analysis and >> then load the polar and eccen. Was this configured as a retinotopy >> analysis? Can you send me the >> >> $ANALYSIS_PHASE/analysis.info file? >> >> doug >> >> >> >> On 12/05/2012 04:12 PM, Julia Foecker wrote: >>> Hi Doug, >>> >>> I tried now several ways to get the maps on the surface: >>> >>> 1. When I am deleting -retinotopy flag and type in: >>> >>> >>>>> tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY >>>>> -analysis $ANALYSIS_PHASE >>> I got the message:no contrast has been specified >>> >>> (I do not have any contrasts in the analysis, just use polar angle maps) >>> >>> >>> 2. I tried to use the commands on the website you referred to, but I do not >>> have -surface in the preproc-sess (see attached) >>> The other commands depend on this preproc-sess command. >>> >>> >>> 3. I tried the following command >>> paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE >>> >>> >>> and I got the errors listed below... >>> >>> I am not sure how to procede. Would you have any further suggestions? >>> Many thanks, >>> Julia >>> >>> Thanks, >>> Julia >> >> >> >> 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. >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Hippocampus volume
by Antonella Kis 06 Dec '12

06 Dec '12

Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much larger number so I wonder which one represents the true total volume in terms of number of voxels. Can you also please advise how can I get differentiated hipocampus segmentation in form of head and body. Thank you. Antonella

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Re: [Freesurfer] Missing Insula and mri_label2vol
by José Ángel Pineda 06 Dec '12

06 Dec '12

Thanks Doug, now it works!! > for mac use > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > > > doug > > On 12/05/2012 05:11 AM, Jos? ?ngel Pineda wrote: > > Hi again, > > > > Sure I did set the permissions for execution, and also for this new > > one I am still having the same error. "/Exec format error. Binary file > > not executable/". I tried this on two macs (OSX Snow Leopard). I am > > still thinking that this is a compilation issue of the script, that is > > just compiled for linux. > > > > Thanks for your help > > > > Try this one > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > > > > On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote: > > > Doug, > > > > > > I am unsure if Jose did this in his attempts to get it to work, > > but I ran this command after downloading and receiving this error > > initially and even after running this command I still receive the > > same error in the Windows virtual machine version of FreeSurfer. > > Any other ideas? > > > > > > Thanks, > > > > > > Cyrus > > > > > > -----Original Message----- > > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of > > Douglas N Greve > > > Sent: Tuesday, December 04, 2012 11:58 AM > > > To: freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] (no subject) > > > > > > Hi Jose, did you set the permissions to be executable? > > > chmod a+x mri_label2vol > > > doug > > > > > > > > > On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote: > > >> Doug, > > >> > > >> I am also curious about this mri_label2vol upgrade. Will this > > work on > > >> the Windows virtual machine version of FreeSurfer? I downloaded > and > > >> placed it in the FREESURFER/bin directory, but when trying to > > run it I > > >> receive an error that states: Exec format error. Binary file not > > >> executable. Thanks for your help. > > >> > > >> Cyrus > > >> > > >> *From:*freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] *On Behalf Of *Jos? > > >> ?ngel Pineda > > >> *Sent:* Tuesday, December 04, 2012 9:07 AM > > >> *To:* freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > >> *Subject:* [Freesurfer] (no subject) > > >> > > >> Thanks Doug, > > >> > > >> I already downloaded the new script for mri_label2vol, but it > > seems it > > >> is just compiled for linux, as I cannot execute it in my Mac. > > If it is > > >> so, could you please upload another compiled for mac, or source. > > >> Thanks > > >> > > >> Jose > > >> > > >> For the missing insula problem, try using a newer version of > > >> mri_label2vol > > >> > > >> > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe > > >> l2vol > > >> > > >> The 2nd problem is not so easy to fix. You might be better > > off using > > >> aparc+aseg.mgz as input to mri_label2vol instead of the > > surface > > >> annotation. > > >> doug > > >> > > >> > > >> On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote: > > >> > Dear experts, > > >> > > > >> > I am registering cortical labels from Talairach > > coordinates to my > > >> > native T1. For doing this, I have run the next script > lines: > > >> > > > >> > > > >> > tkregister --targ brainmask.mgz --mov > > highres_brain.nii.gz --reg > > >> > T1FS2Highres.dat --regheader --noedit > > >> > > > >> > mri_label2vol --annot rh.aparc.annot --temp > > highres_brain.nii.gz > > >> --reg > > >> > T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject > > FS --proj > > >> > frac 0 1 .1 --fillthresh .3 > > >> > > > >> > and the same for the left hemi. > > >> > > > >> > However I am finding two problems at the result. First > > Insula is > > >> > missing for both hemispheres, and second the cortical > > ROIs have the > > >> > shape of the figure attached, e.g. there are many voxels > > empty > > >> > > > >> > Im?genes integradas 1 > > >> > > > >> > I found in previous topics, that the mri_label2vol, was > > updated > > >> as it > > >> > left last volume from the list out of the conversion. I > > tried to > > >> > download it, but it is just compiled for linux, and > > since Im working > > >> > with mac I am not able to run it. Could you please give > > me any > > >> > comments to solve the problem with the missing voxels. > > >> > About the problem with the insula, the other option is > > to just > > >> extract > > >> > it with mri_annotation2label, but if I could get the > > mri_label2vol > > >> > working correctly it would be better. > > >> > > > >> > Thanks a lot > > >> > > > >> > Jose > >

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