Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

display SPM results on inflated surface?
by Schoot, Lotte 15 Feb '17

15 Feb '17

Hi all, I was wondering if you knew of a way to display SPM results onto the inflated surface in Freesurfer. I have tried using SurfRend but there seem to be problems which might be due to the fact the results are obtained with SPM12 and SurfRend was designed to work with SPM5. Thanks, Lotte

2 1

recon-all exited with ERRORS
by Dayanne Ferreira Ayres 15 Feb '17

15 Feb '17

Good morning, I tried to process a patient with the command below after editing it: Recon-all-all -sd / Applications / freesurfer / subjects -no-isrunning -subjid ArlindoRibeirodaSilvaFilhoADRIANO_2009 The file with the error log follows in the attachment. Freesurfer version: 5.3 Platform: MAC OS X yosemite, version 10.10 Att, Dayanne Ayres

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LGI error/Matlab/ a qestion for Douglas Greve
by aral ahmadi 15 Feb '17

15 Feb '17

From: Douglas N Greve So ismac.m is not defined in your matlab implementation? What version of matlab are you using? What kind of computer are you running on? Aral's answer: I am working through VPN and connect to a Linux server using my laptop (Thinkpad2011). Not sure which version of Matlab, this freesurfer5.3 home directory uses, but I have matlab2010 opened on linux when I ran LGI command. although in job output file, it shows a warning that Matlab starting without a display, then it says <MATLAB> copyright 1984-2005 the Mathwork. Inc, version7.1.0.183 (R14) service pack3, Aug2,2005 Thanks, Aral aral ahmadi wrote: > > Dear experts > > I have a question regarding Freesurfer- LGI error I got during running > LGI after all recon steps been ran with no problem. you could see the > error below. > > *reading filled volume... > * > > *??? undefined function or variable 'ismac'.* > *error in -->load_mgh at 68* > * > * > *if(strcmp(computer,'MAC') || strcmp(computer,'MAC') || ismac)* > * > * > *error in -->MRIread at 87* > * > * > *[mri, voi, M, mr_parms, volsz] = load_mgh (fspec, [], [], headeronly);* > * > * > *error in --> make outer-surface at 24* > * > * > *vol = MRIread(filled_volume);* > ** > *>> ERROR:make _outer_surface did not creat output file > 'net/storage1/usr2/onrc/home/p2/Aahmadi/onrc/data/Aral-july/test/subject* > *Linux compute31 2.6.32-504.12.2.e16.*86_64 #1 SMP Wed Mar11 UTC 2015 > 86_64 86_64 GNU/Linux* > * > * > *recon-all -s S1091RPY existed with Errors at thu jan19 2017* > * > * > The error is ...Undefined function or variable 'ismac' - matlab is > expecting that variable to be defined (it's trying to detect the OS, > whether Linux, windows/ Mac), but it isn't. * > * > > I appreciate if you give me your advice on this issue. > > Thanks, > > Aral > >

2 1

Converting Surface Masks to Labels
by Rita Loiotile 15 Feb '17

15 Feb '17

Hi, I'm sorry for what seems like a trivial question. I couldn't find this answer in the tutorials or old archive. I have statistical data in the surface that I have thresholded and binarized to form a mask. I can load the mask as an overlay in tksurfer. My understanding is that you need to turn files into labels in order to change the color display in tksurfer. Is there a command that takes in a shape/surface binary file and converts to labels? I came across this (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-March/017668.ht…) email from Doug, but it looks like I don't have mri_seg2annot in this freesurfer release. More broadly, I would like to tksurfer to display several masks at once, in different colors, using the command line. My understanding is that I would then use mris_label2annot to put all the labels together. When using this function, does the input order of the labels determine the number reference for the color in the Lookup table? What happens in the case where some labels overlap? Thank you in advance, Rita

3 2

bbregister
by John Anderson 15 Feb '17

15 Feb '17

4 5

Coordinates in different modality and space
by Ting Qi 15 Feb '17

15 Feb '17

Dear freesurfer experts, I have some questions about the coordinates conversion, and the relationship between several types of coordinates. First of all, I’d like to confirm whether the coordinates reported in the results summary are based on MNI305 space? Second, I plan to combine multi-modalities data, therefore I would like to use the peak vertex in the surface as a seed to do additional volume-based analysis. I have the vertex index, vertex ras, MNI coordinates reported in the summary text, but how can I get the correct and corresponding volume coordinates in MNI space, particularly in MNI152? I read the page about the freesurfer coordinate system, they mentioned several cases about the transformation, but I still cant figure out what is the correct way in my case. Moreover, I tried the mni305 to mni152, but when I double checked the coordinates in mni152 space, the peak was no longer corresponds to the region reported in the mni305 space. So I sure there must be something wrong. Finally, would anyone offer me a explanation about the relationship between surface RAS, volume RAS, MNI* RAS, Vertex MNI, Volume MNI coordinates? It quite confused me. Thanks in advance, Best regards, Ting

2 1

Normalization of external regressors
by Reza Rajimehr 15 Feb '17

15 Feb '17

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

2 1

PET ROI analysis
by Donatas Sederevicius 15 Feb '17

15 Feb '17

?Hello FreeSurfer Developers, I have done partial volume correction of PET data as described in PETSurfer stream. Now, I want to extract a mean intensity value of my ROI for each subject. This ROI is defined in the fsaverage space and saved as a label. What would be the best way to do it? Should I start from mri_label2label command to map the label to the individual anatomical space or there is another, maybe easier way to do it? Thanks in advance. -Donatas

2 1

Freesurfer v6.0 / Developer version GPU implementation
by Francis Tyson Thomas 15 Feb '17

15 Feb '17

Hi, I'm trying to reduce the freesurfer runtime as much as possible and I was wondering if the GPU flags still work for recon-all in Freesurfer v6? If not is it possible to use the developer version to have it running? Also, if I follow the second approach would the results be the same as that obtained through CPU implementation? Thanks, Tyson

2 2

Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 15 Feb '17

15 Feb '17

Hi Experts! Quick question: is it possible to re-scale intensities relative to the full brain atlas? Details: Per step 3 of the following tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer I wanted to re-scale the the intensities relative to the full brain atlas. The command: --no-rescale removes scaling relative to the Pons and the command: --rescale <Ids> rescales the intensities relative to the region determined by Ids. Would listing all the regions on the --rescale command be the right approach to rescale the intensities relative to the atlas? If so, how do I determine which Ids is which? Thank you in advance! -Anderson

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Freesurfer February 2017