Re: [Freesurfer] PVE correction tool on Freesurfer 6

the response is in the body f the mail On 7/18/16 9:27 PM, Lee Subin Kristine wrote: Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as always, Subin

Re: [Freesurfer] PVE correction tool on Freesurfer 6

Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as always, Subin 보낸 사람: Douglas N Greve 대신 freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] vtk to mgz file

What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz Cheers Bruce > On Jul 18, 2016, at 1:19 PM, Abbie McNulty wrote: > > So we were able to figure out how to segment the different parts of the

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

And I would say if you want to do T1w/T2w myelin mapping the T2w scan will give you more contrast for that, as the fluid inversion does seem to reduce your contrast for myelin some (though it may increase your contrast for CSF). FLAIR can be useful for other things (like seeing some kinds of

Re: [Freesurfer] mri_segstats

Register the suvr to the anatomical (mri_coreg) then use mri_vol2vol On 7/18/16 6:58 PM, Alshikho, Mohamad J. wrote: > Thank you Doug, > Kindly how can I make the suvr and the anatomical images in the same slice? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] Checking segmentations with aseg.mgz

Hi Reema you should visualize it over the norm.mgz. The brainmask and brain will wash out many low contrast borders (e.g. thalamus, pallidum) cheers Bruce On Mon, 18 Jul 2016, Reema Jayakar wrote: Hello FS Listserv members, With regard to checking amygdala segmentation, is it appropriate

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

Hi Michelle that's a tough question. We don't have a ton of experience with it one way or the other, but if I had to pick one I would pick FLAIR as long as you are getting a 3D FLAIR with around 1mm voxels cheers Bruce On Mon, 18 Jul 2016, Michelle T Kassel wrote: Hello,  I am

Re: [Freesurfer] mri_segstats

Thank you Doug, I used the command fslswapdim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alshikho, Mohamad J. Sent: Monday, July 18, 2016 6:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

Re: [Freesurfer] mri_segstats

Thank you Doug, Kindly how can I make the suvr and the anatomical images in the same slice? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 18, 2016 6:56 PM To:

Re: [Freesurfer] mri_segstats

Your suvr is axially sliced whereas the anatomical is corronally sliced. They must be in exact pixel-for-pixel alignment for mri_segstats to work. On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote: > Thank you Doug! > > Attached is a report for one of the subjects showing how the cerebellum >

Re: [Freesurfer] mri_segstats

I sent the files (wmparc.mgz and the functional image) -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 18, 2016 6:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

Re: [Freesurfer] mri_segstats

I'm at a loss as to why that is the case. Can you send the PET.anat.mgz and wmparc.mgz to our filedrop? On 07/18/2016 06:14 PM, Alshikho, Mohamad J. wrote: > Thank you Doug! > > Attached is a report for one of the subjects showing how the cerebellum > structures have zeros for the mean, SD ,

Re: [Freesurfer] mri_segstats

Thank you Doug! Attached is a report for one of the subjects showing how the cerebellum structures have zeros for the mean, SD , ...etc ( red circles) Also if we scroll down ( not included), all the cerebellum parcellates ( white and cortex) are zeros. I have this issue with 70 % of the

Re: [Freesurfer] FSGD error: class Input not defined

You have a rogue non-ascii character between HM-HR10-002Rest and Group1 (between others). Make sure you create your fsgd file in a simple ascii text editor. On 06/23/2016 01:48 AM, Jarek Rokicki wrote: > Dear Freesurfer experts, > > I am trying to perform the resting state fMRI analysis as in:

Re: [Freesurfer] mri_segstats

Thank you Doug! Attached is a report for one of the subjects showing how the cerebellum structures have zeros for the mean, SD , ...etc ( red circles) Also if we scroll down ( not included), all the cerebellum parcellates ( white and cortex) are zeros. I have this issue with 70 % of the

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

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 wrote: > The file has not been anonymized. > > Thanks, > > Ismail > >> On Jul 5, 2016, at 11:20 AM, Douglas N Greve >> wrote: >> >> can you answer

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

It did, I removed 2 of them and it's running fine now. Thanks! Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 5:48 PM To:

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

Check the contents of /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname It may have the subjectname repeated 3 times On 07/18/2016 05:45 PM, Hibert, Matthew Louis wrote: > Attached. I took a quick look and it seems that I wrote the subject name 3 > times, on new

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

Attached. I took a quick look and it seems that I wrote the subject name 3 times, on new lines, to the subjectname file. I removed 2 of them and re-ran selxavg3-sess and it appears to be working. Thanks for the help Doug. Matt From:

Re: [Freesurfer] DeMean Flag

The DeMeanFlag in what tool? On 07/08/2016 05:16 AM, Clara Kühn wrote: > Dear Freesurfer experts, > > is there an explanation somewhere for the DeMeanFlag? I can't find it in the > wiki but I would like to use it to demean my covariates for the GLM and LME. > > Cheers > Clara > -- Douglas N.

Re: [Freesurfer] mri_segstats

What do you mean you got 0s only for the cblum segs? Did all other segs have non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline? On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote: > Thank you very much Doug for your answer. > Kindly I have one more question: > Although

Re: [Freesurfer] Question about NULL event with Optseq2

Some of this might be fixed with a newer version of optseq: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2 The long last NULL might not be fixed. It is just hard to get all the things to add up to get the right amount of time, so it time is left over, it adds it to the

Re: [Freesurfer] Inquiries about thickness and lgi group analysis

Well you can start by telling us what you did. There is not much info down there On 07/14/2016 10:40 AM, Mahtab Farahbakhsh wrote: > Dear FreeSurfer, > > I am doing group analysis for thickness and LGI values. I have just > got the output and the output of both analyses (sig.mgh file view in >

Re: [Freesurfer] mri_glmfit error

I can't tell from the glmfit command line what you are trying to do. Generally, the GLM is run on group data and you specify an average brain (eg, fsaverage) as the --surf. On 07/14/2016 06:10 AM, Chatzi, Vasiliki wrote: > > > Dear Developers, > > > I am trying to run the mri_glmfit command and

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

Can you run the command below and send me dng.log? register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update |& tee dng.log On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: > Hi All, > I'm running into an error

Re: [Freesurfer] Comparing between a group of subject

Use the GLM approach (cross-sectional, not longitudinal). You don't need a variable to regress against, just set up two groups, with one group being your single subject. Though I'm not sure what you want to gain out of this. On 07/15/2016 04:08 PM, Aman Montazeri wrote: > Hi Freesurferes, > >

Re: [Freesurfer] BrainSegVolNotVent

I think you may be using a very old version of mri_segstats. The version 5.3 mri_segstats gives: # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1290472.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1279674.00, mm^3

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

It does not look like the variables are demeaned (your FSGD file below) Variables Age eTIV EnglishParityRT Input Math_5001m Monolingual_male 18 1865790.30866 -8952.208 Input Math_5002m Monolingual_female 19 1520429.68796 -4605.208 Input Math_5003m Monolingual_male 19 1749716.72939

[Freesurfer] Checking segmentations with aseg.mgz

Hello FS Listserv members, With regard to checking amygdala segmentation, is it appropriate to overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz on norm.mgz? I am aware of the general rule of thumb that editing the subcortical segmentations generally is not

[Freesurfer] T2 vs. T2-FLAIR update

Hello, I am beginning a new study and would like to determine the optimal T2 acquisition parameters for improved pial surface results from FreeSurfer. I am wondering if there is a difference in using a T2 or T2-FLAIR. I have found a discussion post from 2014 which provided useful information

Re: [Freesurfer] BrainSegVolNotVent

Hi Doug, Thanks for your reply. I just sent you this subject's directory via file drop. Please note that there are two aseg.stats files under the 'stats' folder: aseg.stats: generated by the mri_segstats command I ran including the --brainmask mri/brainmask.mgz --brain-vol-from-seg flags.

Re: [Freesurfer] registering to fsaverage

Hi Doug My apologies for the delay - I just returned from vacation. Ok, so when I take a volumetric spam created using minc tools and create an overlay from it using mri_vol2surf, the min and max seems to be between 1 and 255. I am wondering if there is any where to change this into a %? When I

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Try running make_average_volume. This will produce an aseg.mgz file with all the ROIs merged across all subjects On 07/13/2016 07:10 AM, Dr Sampada Sinha wrote: > Dear Bruce, I am trying to generate the following picture (please see > attached) for eod vs lod groups. Can you please tell me

Re: [Freesurfer] BrainSegVolNotVent

That does look suspicious, esp since BrainSegNotVent should be smaller than BrainSeg. Can you tar up the subject and send it to me? It may be some strange incompatibility with v5 On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote: > Hello Doug and Freesurfers, > > I am trying to compute a

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

Hi Doug, Thank you for your response. The current fsgd file I sent you was with the covariates demeaned x 100, as I saw you recommend that to someone else. We previously tried doing just the demeaned values without multiplying by 100, and that still had the badly scaled error. Do you think we

[Freesurfer] vtk to mgz file

So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk

Re: [Freesurfer] Re Re: Checking Surfaces vs. aseg outputs

nope, I would start with the aseg and only check other things if the ventricles aren't accurate On Mon, 18 Jul 2016, Tamara Tavares wrote: Thank you again Bruce. Since I am primarily interested in ventricular volume, do you think it is necessary to check the the brainmask.mgz for bright or

[Freesurfer] can not find module 'dev'

Dear All, I recently tried to gain access the read-only CVS source-code repository, however, I have this kind of error: cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules anyone have idea what is going on here? Thank you so much! Best, Yun Wang

Re: [Freesurfer] PVE correction tool on Freesurfer 6

On 07/12/2016 11:03 PM, Lee Subin Kristine wrote: > > Hi Doug, > > > Thanks a lot for the page! It was very helpful. > > > I have a few questions about one of the commands and a question for > one of the output files. > > > 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg >

Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31

Hi Bruce, Thank you for your quick reply. We are primarily interested in ventricular volume but we may look at other areas in the future; this is why I thought it would be a good idea to check the surfaces. Is the reasoning why the surface outputs vs. aseg outputs should be checked is because

Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31

Hi Tamara no, the surfaces shouldn't affect the volume of the ventricles, so if that is all you care about just inspect the aseg. cheers Bruce On Mon, 18 Jul 2016, Tamara Tavares wrote: Hi Bruce, Thank you for your quick reply. We are primarily interested in ventricular volume but we may

[Freesurfer] Integrate SPM activation maps to FreeSurfer structural volumes

Dear FreeSurfer, I am trying to register my SPM activation maps to the structural data of each subjects. Except for the commands I could find for the registration, I could not find a guide on the registration of activation maps from SPM to FreeSurfer. Would you please guide me how I should do

Re: [Freesurfer] Beta-Zero Correction - No Phase File

You can extract frames from a multi frame file with mri_convert input.nii.gz --frame 0 output.frame0.nii.gz On 07/12/2016 02:29 PM, Afzal, Afsana wrote: > Hi, > > I'm working with a dataset that outputs only one file (not two > separate mag and phase files) for the fieldmap. The data was also

Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted

When FS reads a series of dicom files, it tries to sort them in time and space so that it can generate the appropriate 4D volume. To do this, it needs to get info out of the DICOM header to determine this sorting. This includes image number and geometry information. If that information is not

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

This is almost surely a problem with scaling as your covariates are huge. Try subtracting the mean and dividing by the stddev before entering into the FSGD file. Compute the means and stddevs across all subjects. doug On 07/11/2016 03:20 PM, Jennifer Legault wrote: > Hi Freesurfer Experts, > >

[Freesurfer] Re Re: Checking Surfaces vs. aseg outputs

Thank you again Bruce. Since I am primarily interested in ventricular volume, do you think it is necessary to check the the brainmask.mgz for bright or dark spots indicating an intensity normalization error? As well, what about a skull strip error such as removal of brain tissue? I have noticed

Re: [Freesurfer] white and pail surface editing

Hi Ri I think you can just run it all as one recon-all command. cheers Bruce On Mon, 18 Jul 2016, Ritobrato Datta wrote: > Hi All, > > We have some subjects who have both wm errors and gm errors. > > Is the following workflow possible > > > Step 1) control points for the white matter edits.

[Freesurfer] white and pail surface editing

Hi All, We have some subjects who have both wm errors and gm errors. Is the following workflow possible Step 1) control points for the white matter edits. DONT RUN recon-all Step 2) add the pial surface edits. DONT RUN recon-all Step 3) Run recon-all to incorporate control points for wm

[Freesurfer] can not find module 'dev'

Dear All, I recently tried to gain access the read-only CVS source-code repository, however, I have this kind of error: cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules anyone have idea what is going on here? Thank you so much! Best, Yun Wang

Re: [Freesurfer] Integrate SPM activation maps to FreeSurfer structural volumes

Hi Mahtab check out bbregister. It should do the trick. cheers Bruce On Mon, 18 Jul 2016, Mahtab Farahbakhsh wrote: > Dear FreeSurfer, > I am trying to register my SPM activation maps to the structural data of > each subjects. Except for the commands I could find for the registration, I >

[Freesurfer] LME contrasts

Dear FreeSurfer experts, I am following the mass-univariate (spatiotemporal) model in the LME tutorial. My design matrix X has the following columns: intercept, time, time², group1, group1*time, group1*time², group2, group2*time, group2*time², sex, age, mean_thickness I actually have 3 groups