[Freesurfer] get non-cortex vertices

Hi freesurfers, I am doing a connectivity analysis on cortical areas. I load the 2d fmri surface file in fsaverage5 space into matlab and I get 20484 vertices for both hemispheres. Some of which are zero because I previously specified to get only the cortex vertices. However, the number of

[Freesurfer] Question about mri_glmfit

*Hello,* *I would like to conduct an analysis using mri_glmfit but I'm getting this error:* *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* *I am appreciated you can help me solve this problem. * *My command was:* mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C

Re: [Freesurfer] Co-registering different source data

I get a different error when I use --regmethod surface (below). I double checked that I am in the correct hemishpere. I'm not sure if it has to do with teh volume I used to draw to ROI or something with how I drew it. Thanks, Anna mri_label2label --srcsubject segfs --srclabel

Re: [Freesurfer] get non-cortex vertices

Hi Douglas, Thanks for your reply. I thought when individual space data is projected onto fsaverage5 space it get wrapped in a common space, so one vertex would correspond to the same area across subjects, like in MNI. I tried to create a group subcortical mask by loading each subject fmri

[Freesurfer] TRACULA results

Hi, I downloaded FreeSurfer development version built on Sep 20. Then I ran the "trac-all" for the same set of DWI data four times. The volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, are different for

Re: [Freesurfer] Co-registering different source data

Hi Anna sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives? thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote: > I have tried multiple variations for my subject directory. I have had it end > at

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

You need to specify --trgsubject ico in mri_vol2surf On 9/28/16 3:01 PM, Jared Zimmerman wrote: > Hi All, forwarding this message along again as I'm still having some trouble > getting this to work. Basically I would like to 1) project processed > residual time-series from the subject-space

[Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall

Hello FreeSurfers, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent

Re: [Freesurfer] Co-registering different source data

Is Testing1.label a surface-based label? If so, use --regmethod surface On 09/28/2016 04:39 PM, Crawford, Anna wrote: > The subject path was > /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf > > From:

Re: [Freesurfer] Co-registering different source data

Can you send me the label? On 09/28/2016 05:54 PM, Crawford, Anna wrote: > I get a different error when I use --regmethod surface (below). I double > checked that I am in the correct hemishpere. I'm not sure if it has to do > with teh volume I used to draw to ROI or something with how I drew

[Freesurfer] mri_glmfit: Hierarchical Regression?

Hello all, I am using mri_glmfit (DODS method) to run a CT analysis with 2 groups and 4 covariates and have a couple of questions regarding the statistical tests performed within the group analyses: 1. Can Freesurfer test the change in model fit or delta R-squared in a hierarchical

[Freesurfer] Projecting processed 4D functional data to individual surfaces

Hi All, forwarding this message along again as I'm still having some trouble getting this to work. Basically I would like to 1) project processed residual time-series from the subject-space volume to the subject-space surface, 2) smooth on the surface, 3) down-sample to FS4 space. To do this

Re: [Freesurfer] Anatomy File Orientation Question

You do not need to specify that. In fact, you should not because it may mess up the orientation. You do not need to add any special arguments to mri_convert. You can also specify .nii instead of .nii.gz On 9/27/16 3:14 PM, Sepeta, Leigh wrote: Hi all, Sorry to re-post: I am trying to

Re: [Freesurfer] optseq help

The command line looks ok. The low efficiency is coming from the low number of events per event type. On 9/27/16 9:52 AM, Alexandre Obert wrote: Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable

Re: [Freesurfer] Question about mri_glmfit

Hi Greve Thanks for your reply, can I have more detail about how to solve my problem. By the way, I may not think it's the problem about covariates. Thank you. Jin 2016-09-28 15:29 GMT-04:00 Douglas Greve : > Try normalizing your covariates (ie, subtract the mean and

Re: [Freesurfer] Co-registering different source data

Try giving it the full path to the label, ie, --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label On 9/28/16 3:47 PM, Crawford, Anna wrote: > Hi, > > Below is the command I entered with the output containing the error. I also > tried different variations

Re: [Freesurfer] Question about mri_glmfit

Hi there, Anyone can help me out? Thank you. 2016-09-28 13:46 GMT-04:00 kinson li : > *Hello,* > > *I would like to conduct an analysis using mri_glmfit but I'm getting this > error:* > > *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* > > *I am

Re: [Freesurfer] Co-registering different source data

Hi, Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be. Thanks, Anna mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel

Re: [Freesurfer] Co-registering different source data

what was your freeview command line, and what did you do to make it crash? On Wed, 28 Sep 2016, Crawford, Anna wrote: > Thank you! that seemed to have worked. I thought I had tried that before, but > must not that. The input/output is below. The new label was created. When I > tried to load

Re: [Freesurfer] Co-registering different source data

can you email me (offlist) the inflated surface and the label you tried to load? On Wed, 28 Sep 2016, Crawford, Anna wrote: > The subject path was > /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf > > From:

Re: [Freesurfer] monte carlo continue/ desktop restarted

There is no way. Yes, you can specify fsaverage for yoursubject On 9/28/16 3:47 PM, miracle ozzoude wrote: Hello Doug, Do you know if there's any command to make it continue from where it stopped in case of future incidents? Also, what does " yoursubject" mean in this code? Can I substitute

Re: [Freesurfer] Co-registering different source data

The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert

I don't understand what the problem is. Can you elaborate? On 9/27/16 12:13 PM, Tamara Tavares wrote: The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and

Re: [Freesurfer] Question about mri_glmfit

compute the mean and stddev of your covariate, subtract the mean from each covariate, and then divide the result by stddev. On 9/28/16 3:47 PM, kinson li wrote: Hi Greve Thanks for your reply, can I have more detail about how to solve my problem. By the way, I may not think it's the problem

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you On Wed, Sep 28, 2016 at 3:49 PM, Douglas Greve wrote: > There is no way. Yes, you can specify fsaverage for yoursubject > > On 9/28/16 3:47 PM, miracle ozzoude wrote: > > Hello Doug, > Do you know if there's any command to make it continue from where it >

Re: [Freesurfer] Co-registering different source data

I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when

Re: [Freesurfer] Co-registering different source data

which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote: > I just opened freeview (just typed freeview into the command line). Then from > inside freeview, under the surfaces tab, I loaded the lh.inflated and > rh.inflated. Also

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

Those are not residuals. If you want residuals, you will need to run mri_glmfit from the command line adding --eres-save. You can get the command line from the mri_glmfit.log file in the glmdir On 9/28/16 10:58 AM, Damien MARIE wrote: Dear FreeSurfers, Sorry for the repost. I’m still

Re: [Freesurfer] monte carlo continue/ desktop restarted

Hello Doug, Do you know if there's any command to make it continue from where it stopped in case of future incidents? Also, what does " yoursubject" mean in this code? Can I substitute it with fsaverage? Thanks Paul mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/rh/cortex \

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert

Hi Tamara can you let us know how big the differences are? thanks Bruce On Wed, 28 Sep 2016, Douglas Greve wrote: I don't understand what the problem is. Can you elaborate? On 9/27/16 12:13 PM, Tamara Tavares wrote: The differences have been found in the outputs from the aseg

Re: [Freesurfer] Question about mri_glmfit

Try normalizing your covariates (ie, subtract the mean and divide by the stddev). On 9/28/16 3:07 PM, kinson li wrote: Hi there, Anyone can help me out? Thank you. 2016-09-28 13:46 GMT-04:00 kinson li >: /Hello,/ /I would like to

Re: [Freesurfer] get non-cortex vertices

It is changing with each subject because each subject's brain is different, and you can't get a subject-specific mask from fsaverage5. Can you load all your data into matlab and then compute a mask based on non-zero voxels? On 9/28/16 1:57 PM, Dorothy Sincasto wrote: Hi freesurfers, I am

Re: [Freesurfer] Co-registering different source data

Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on

Re: [Freesurfer] Sulcus depth

Dear FreeSurfer Team, I have an additional question about the ?h.sulc. [mris_anatomical_stats can do this if you specify sulc as the "thickness" file] your explaination means that instead of the mris_anatomical_stats -l -t *lh.thickness* -b -f lh I can use these command with change the -t

[Freesurfer] question about mris_anatomical_stats

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference

Re: [Freesurfer] Sulcus depth

yes, I believe so Bruce On Wed, 28 Sep 2016, Hanbyul Cho wrote: Dear FreeSurfer Team, I have an additional question about the ?h.sulc. [mris_anatomical_stats can do this if you specify sulc as the "thickness" file] your explaination means that instead of the mris_anatomical_stats -l -t

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

you can actually skip the ico thing and just use --trgsubject fsaverage6 On 9/28/16 7:06 PM, Jared P Zimmerman wrote: Thanks Doug, This does seem like it will do the right thing, but it’s failing because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject in my

[Freesurfer] How to parcellate the whole white matter into different lobules using Freesurfer ?

Dear freesurfer experts: I was wondering if it would be possible to parcellate whole white matter into different lobules (e.g. white matter in frontal lobule, parietal lobule, temporal lobule, and so on) by using Freesurfer ? My goal is to compute the white matter volume, as well as FA

[Freesurfer] mgz file format

Hi, When using mri_convert to create 001.mgz from dicom that have *not* been anonymized does any patient, institution, study description etc information get transferred into the 001.mgz? Thanks. ___ Freesurfer mailing list

Re: [Freesurfer] TR: volume to surface for ROI already in orig space

Thanks a lot Bruce! This is extremely useful! A. De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Bruce Fischl Envoyé : mardi 27 septembre 2016 17:23:30 À : Freesurfer support list

[Freesurfer] FreeSurfer on MP2RAGE

Dear all, We have been working quite extensively with Freesurfer over the years. We are now starting to collect a new large cohort and we are about to decide which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, headcoil 20 Chanel). When we visually inspect the images we

[Freesurfer] monte carlo continue/ desktop restarted

Hello experts, I was running 1 monte carlo simulation before my desktop automatically restarted, does anyone know a command to continue from where it stopped? The simulation for left hemisphere stopped at 9146/1 and right hemisphere at 9125/1. Thank you Paul

Re: [Freesurfer] monte carlo continue/ desktop restarted

I would just use what was created. There is nothing magical about 10,000 iterations. A few iterations short won't make any difference. On 09/28/2016 10:35 AM, miracle ozzoude wrote: > Hello experts, > I was running 1 monte carlo simulation before my desktop > automatically restarted, does

[Freesurfer] REPOST cluster feature extraction from qdec output

Dear FreeSurfers, Sorry for the repost. I’m still trying to extract the residuals of cortical surface area from a qdec analysis with two factors (2 levels) and 2 covariates. I tried this command line: mri_segstats --in

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you Doug Paul On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve wrote: > I would just use what was created. There is nothing magical about 10,000 > iterations. A few iterations short won't make any difference. > > > On 09/28/2016 10:35 AM, miracle ozzoude