Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on? On 7/19/16 1:57 PM, Koubiyr, Ismail wrote: I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header. Here is the version of FS I

Re: [Freesurfer] registering subject pial to fsaverage

I don't understand what you did or what the problem is. Can you elaborate? On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote: Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that

Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

Thanks responding Doug! I am interested us using centrum semiovale as reference region. Is there a way I can save the unsegmented white matter [5001& 5002] during the gtmseg step or what would be its equivalent label in the gtm_pvc results table? Thanks, Pradeep On Thu, Jul 7, 2016 at 11:20 AM

Re: [Freesurfer] question about voxel size

Hi Dorsa it works best with 1mm data as that was what it was designed for. Higher res can reveal unmodeled structures (e.g. stria of Gennari) that make things less accurate cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Here it is. Also can you explain why the algorithm wo

[Freesurfer] registering subject pial to fsaverage

Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below i

Re: [Freesurfer] Fwd: question about voxel size

what is a "3TS" image? Do you mean it was acquired at 3T? What sequence and what parameters (TE/TR/TI/TD/flip angle)? cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > Hi Bruce, > that is a 3TS T1 weighted image and is taken after the patients have taken > the contrast medium. I ha

Re: [Freesurfer] Fwd: question about voxel size

Hi Bruce, that is a 3TS T1 weighted image and is taken after the patients have taken the contrast medium. I have played with the intensities in Analyze and this is the best I could get. Do you have any suggestions for getting better contrast? Thank you Dorsa On Tue, Jul 19, 2016 at 4:29 PM, Bruc

Re: [Freesurfer] mriBuildVoronoiDiagramFloat - argument out of domain

I'm not sure what's going on. If you tar and gzip one of the subject directories we'll see if we can replicate and fix it Bruce On Tue, 19 Jul 2016, Uquillas, Federico D'Oleire wrote: Hi Bruce, Thank you for the quick reply. Please see below: Volume information for brainmask.mgz ty

Re: [Freesurfer] question about voxel size

Hi Dorsa without the norm.mgz I have no way to evaluate the accuracy of the aseg. cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Yes That is a possible and I am going to talk to my group about it. I have attached the brain segmentation and the aseg.stats. I'll be happy to hear

Re: [Freesurfer] vtk to mgz file

sorry, perhaps someone else can help you with this. I haven't used plotmesh. cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: Perfect. now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y') On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl wrot

Re: [Freesurfer] vtk to mgz file

Perfect. now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y') On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl wrote: > > > [aseg,M,mr] = load_mgh('aseg.mgz'); > ind = find(aseg == 16); > > > that will give you the indices in the aseg volume of the vo

Re: [Freesurfer] vtk to mgz file

If i just wanted to plot the brainstem On Tue, Jul 19, 2016 at 12:00 PM, Abbie McNulty wrote: > Perfect. > now if I wanted to use plotmesh with this, what would the variables be for > x and y: plotmesh('x,y') > > On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl > wrote: > >> >> >> [aseg,M,mr] = l

Re: [Freesurfer] vtk to mgz file

[aseg,M,mr] = load_mgh('aseg.mgz'); ind = find(aseg == 16); that will give you the indices in the aseg volume of the voxels that have the brainstem label (16). Then you can do what you want with it. The label came from $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Tue, 19 Jul 20

Re: [Freesurfer] vtk to mgz file

So say I load aseg.mgz into matlab and I want to extract the brainstem in matlab to plot its own volumetric mesh vs. the entire brain, how would I extract the brainstem in matlab? On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl wrote: > but why not just load the aseg.mgz or whatever volume you ar

Re: [Freesurfer] mriBuildVoronoiDiagramFloat - argument out of domain

Hi Bruce, Thank you for the quick reply. Please see below: Volume information for brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0

Re: [Freesurfer] mriBuildVoronoiDiagramFloat - argument out of domain

hmmm, no, that's odd. Did you do anything outside of FS on any of the volumes? Try running mri_info on aseg.presurf.mgz, brainmask.mgz and norm.mgz and send us the output cheers Bruce On Tue, 19 Jul 2016, Uquillas, Federico D'Oleire wrote: Dear fellow Freesurfer users,  I have 4 jobs that

Re: [Freesurfer] question about voxel size

Hi Dorsa why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-r

Re: [Freesurfer] question about voxel size

Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by

Re: [Freesurfer] vtk to mgz file

but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can extract with the find command cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: I attached the page in the last message, maybe it didn't show.

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header. Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514 Do you think it might be related ? Thanks again. Ismail On Jul 19, 2016, at 1:27 PM, Douglas N

Re: [Freesurfer] vtk to mgz file

I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes This link describes the process that am I am working with, and there is a

Re: [Freesurfer] vtk to mgz file

Hi Abbie I'm not sure what page you mean. The segmentations start life as an .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever segmentation you are interested in) into matlab directly cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: Hi Bruce, So when I'm at

Re: [Freesurfer] question about voxel size

Hi Dorsa are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Ha

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

What is your exact command line? The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run mri_probedicom --i MR.1.3.12.2.1107.5.2.1

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Hi Doug, That’s weird because I can’t convert it using only mri_convert, here is the error I get : WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERR

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored wi

Re: [Freesurfer] recon-all exited with erros

Hello Salem, Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl v5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and that version of perl. The issue has been fixed in the development version o

Re: [Freesurfer] 3 analyses questions

On 07/19/2016 05:11 AM, Caroline Beelen wrote: > > Dear FS team, > > I would like to correct for multiple comparisons after I run > command-line GLM analysis on aparc.stats tables (my ROI’s are few > regions from DK-atlas). I tried to do the Monte Carlo simulation but > get an error that a mas

Re: [Freesurfer] question about voxel size

Hi Dorsa, well visual inspection is always a good indicator. Also you could have a look at the QA Tools (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools). I haven’t tested them though. Other than that, I wouldn’t know of any objective method to validate your results. Probably someone else ca

Re: [Freesurfer] question about voxel size

Hi Dorsa, until version 6 of FreeSurfer is released you could try to follow the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) which should enable you to process the data in its native resolution. With FreeSurfer v6 this workaround will not be necessary anymore, as the proces

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Bruce, thanks for the quick reply. I'll try it out once I have a bit of memory available and let you know if it helped. Best, Falk -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesend

Re: [Freesurfer] TRACULA group stats visualization

Hi Anastasia, I thought I should let you know that this issue has now been resolved. We specified the base ID's/ subject ID's incorrectly in the config file! Sorry for the confusion. Now our group output looks correct. Thanks for your help, Derek From: f

[Freesurfer] question about voxel size

Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari __

Re: [Freesurfer] Bug in Freesurfer Installation

Of course. I should have known. That fixed the problem. Thank you very much Aman and Z.K. Best, Sherryse ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] can not find module 'dev'

Use the git repo instead: http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page -Zeke On 07/18/2016 11:51 AM, Yun Wang wrote: > Dear All, > > I recently tried to gain access the read-only CVS source-code > repository, however, I have this kind of error: > > cvs server: ca

Re: [Freesurfer] Bug in Freesurfer Installation

Try either opening up the permissions in $FREESURFER_HOME/subjects, or copy the file to your home directory and executing the mri_convert command there instead. By default mac uses root permission for programs installed under /Applications -Zeke On 07/15/2016 05:40 PM, Sherryse Corrow wrote:

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Hi Doug, It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks. Ismail > On Jul 18, 2016, at 6:14 PM, Douglas N Greve > wrote: > > Is this still a problem? If so, can you upload the dicom files to our > file drop? > > On 07/05/2016 11:24 AM, Koubiyr, Ismail wr

Re: [Freesurfer] T2 vs. T2-FLAIR update

In my experience, if the only goal is to improve the pial surface reconstruction, it is better to use a T2-SPACE-FLAIR than a T2-SPACE. Whenever possible, we acquire a bandwidth matched T2-SPACE-FLAIR at approximately the same resolution as our T1 and use this with our Freesurfer reconstruction

Re: [Freesurfer] Request for new mri_tessellate (error: max vertices 1000000 exceeded)

Hi Bart 1M is really not enough for you? How many would you need? I'll try to find the time to make it dynamically allocated and configurable one of these days Bruce On Tue, 19 Jul 2016, Ferguson, B. wrote: Dear Freesurfer team, I am running Falk Luesebrinks hires recon, and am running i

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk I think openmp will help with this in V6, but probably not before Bruce On Tue, 19 Jul 2016, Falk Lüsebrink wrote: Hi all,   I’m currently processing a 250 µm MPRAGE with a dev build from mid of May. Running recon-all with default parameters ran flawlessly. Afterwards I added the

[Freesurfer] Request for new mri_tessellate (error: max vertices 1000000 exceeded)

Dear Freesurfer team, I am running Falk Luesebrinks hires recon, and am running into the error of "mri_tessellate: max vertices 100 exceeded" when I run the command line "recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT" o

[Freesurfer] 3 analyses questions

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on aparc.stats tables (my ROI's are few regions from DK-atlas). I tried to do the Monte Carlo simulation but get an error that a masking-file is missing. In general, how could I correct for mult

[Freesurfer] recon-all exited with erros

Hi I’m trying to run free surfer on a set of T1 images. I tried to do it on one patient first before running it on the whole dataset. I ran the recon-all with the -all option I had an error message one minute after it has been launched. It stopped at the mri_nu_correct.mni. Could you please advise