Re: [Freesurfer] Qdec-correction for multiple comparison

Hi Doug, thank you veru much for the answr. Please what do you mean by " an emperical question that depends on your data"? For example:    I have two groups of participants. I ran cortical thickness analysis in Qdec to study the differnce between the groups in cortical thickness:  1. Monte

[Freesurfer] mri_segstats

Dear FS experts, I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean PET signal for every parcellate and segment in the atlas "wmparc.mgz". Which one of the following commands is more accurate? 1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab

Re: [Freesurfer] question about exporting volumes

what do you mean isolate? what do you mean export? You can create a binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49 --o thalamus.mask.nii.gz On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote: > > > > Hi, > > I was able to segment the MRI successfully, now I am trying

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

Hi, This is a repost. Would anyone have a solution to this problem ? Thanks for your help. Best, Ismail > On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail wrote: > > The file has not been anonymized. > > Thanks, > > Ismail > >> On Jul 5, 2016, at 11:20 AM, Douglas N

Re: [Freesurfer] fslaverage/MNI coordinates

Hi Doug, Thank you so much! Because I will do the analysis using SPM, I need the coordinates in MNI152 space. I found a transformation between them: M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840

[Freesurfer] question about exporting volumes

Hi, I was able to segment the MRI successfully, now I am trying to isolate the thalamus and export it out of FS as a volume. Is there a way to do that in FS? Thank you Dorsa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] fslaverage/MNI coordinates

Hi Baojuan, that coordinate will be mni305 space. Is that what you want? On 07/06/2016 04:17 PM, Li, Baojuan wrote: > Dear Freesurfer experts, > > > I am using MNE (with MEG data) to define my ROIs for a connectivity > analysis. I am going through the following steps to get the MNI >

[Freesurfer] fslaverage/MNI coordinates

Dear Freesurfer experts, I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions: 1. Morph the subject's brain to fslaverage; 2. Load the inflated surface of fslaverage to MNE analyze; 3.

Re: [Freesurfer] question about white matter edits

Hi Rito the control points you have look like they are in voxels that contain some gray matter, which will probably make things worse. YOu need to identify why you are missing that part of the surface. Is the dark stuff there labeled as white? Maybe it's a topological defect that gets filled

[Freesurfer] Design Matrix Creation

Hi Doug, I just wanted to make sure that we were on the same page. I may have been a little unclear in what I would ideally like to do. For #2 what I would like to do is take into account age slopes and total intracranial slopes for gender, and age slopes and total intracranial slopes for

Re: [Freesurfer] question about white matter edits

Hi, The missing sulcus may be a consequence of the topology correction going awry.  Check the “nofix” surface to see the surface before topology correction.  If the topology correction is the problem, you’ll need to edit the wm.mgz.  There is an example on the FS tutorials.

[Freesurfer] LGI Summary Statistics

Freesurfer Support, I have seen previous message threads on extracting LGI measurements across ROIs, however I have yet to find anything which would provide a summary LGI across an entire hemsphere. Other measurements like cortical thickness have a measurement like this. Is there a measurement

Re: [Freesurfer] Seed based volume output to surface

The output L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz is already on the surface. if you need the output as text, you can run mri_convert sig.nii.gz output.txt --ascii or use --ascii+crsf --ascii save output as ascii. This will be a data file with a single

Re: [Freesurfer] Design Matrix Creation

I did not get the same matrix. Here's how I would do it Columns 1-16 model the intercepts for all your classes Columns 17-20 model the ages for your gender-x-diagnosis subclasses Columns 21-24 model the ICV for your gender-x-diagnosis subclasses On 07/06/2016 02:04 PM, Timothy Hendrickson

Re: [Freesurfer] mris_preproc subject-volume mismatch

Ah, the problem is with using an lta with 5.3 mris_preproc. I've put version 6 mris_preproc here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc try that and see if it works. Alternatively, you could convert the lta files to register.dat files On 07/06/2016 02:02 PM,

[Freesurfer] Design Matrix Creation

Freesurfer Support, Thank you for your support with my previous line of questions regarding design matrix creation. I have manually created another design matrix and want to ensure that I designed it correctly. An example of my FSGD file is as follows below: Class SITE 1-Male-Control Class SITE

Re: [Freesurfer] FSFAST- Cerebellum

What is the problem with the orientation? The little letters indicate that the orientation is correct. fslview ignores the orientation when displaying so it might come out upside down. On 07/05/2016 01:35 PM, Sabin Khadka wrote: > > Hi Doug, As you suggested I mapped fmri into the anatomical

Re: [Freesurfer] mris_preproc subject-volume mismatch

Hmm, it says that there is one frame in each of the subjects. 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: Wednesday, July 06, 2016 1:54 PM To:

Re: [Freesurfer] Intensity stats question

that looks right. You might want to call the output something else so that you don't overwrite the default FS output On 07/06/2016 01:55 PM, Sabrina Yu wrote: > > Hi, > > > Thanks for the quick reply. I just want to confirm that my command is > correct for changing the input volume to orig.mgz:

Re: [Freesurfer] Intensity stats question

Hi, Thanks for the quick reply. I just want to confirm that my command is correct for changing the input volume to orig.mgz: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/orig.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/orig.mgz --in-intensity-name orig

Re: [Freesurfer] mris_preproc subject-volume mismatch

It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each On 07/06/2016 01:39 PM, Raney, Talia L. wrote: > mris_preproc --target fsaverage --hemi lh --iv >

Re: [Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

It would be something like mris_apply_reg --src lh.data-from-fsavgsym.mgh --streg $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg $SUBJECTS_DIR/yoursubject/surf/lh.fsaverage_sym.sphere.reg --o lh.data-from-fsavgsym-on-yoursubject.mgh On 07/04/2016 10:34 AM, Ali-Reza Mohammadi-Nejad wrote: >

Re: [Freesurfer] Qdec-correction for multiple comparison

There is no recommendation between FDR and monte carlo. The question of which one is "better" is an emperical question that depends on your data. On 06/29/2016 06:38 AM, John Anderson wrote: > Dear FS experts, > I will re post this thread again looking for your help and support: > I ran cortical

Re: [Freesurfer] Applying the lta transformation to PET image | mri_coreg | mri_segstats

use mri_vol2vol to map the pet into the anatomical space On 06/28/2016 01:48 PM, Pradeep wrote: > Hello All, > > I am trying to extract the SUV values a PET image > > mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET > --ctab-default > > since rPET is supposed to be coregistered

Re: [Freesurfer] Unsupported slice timing pattern 5 in version 5.3.0

try this version and let me know if it works. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert If not, please send me the dicom via filedrop below On 06/30/2016 05:45 AM, Leonardo Tozzi wrote: > > To Whom it may concern, > > > I have tried to run the recon-all pipeline

Re: [Freesurfer] mris_preproc subject-volume mismatch

mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out

Re: [Freesurfer] Not able to find file in gtmseg

The subject name is the FreeSurfer subject name assigned when you ran recon-all to analyze the T1 anatomical MRI images. BTW, you need everything in native space to run the pipeline. doug On 06/30/2016 12:25 AM, Lee Subin Kristine wrote: > Dear FreeSurfer experts, > > Hello, > I am trying to

Re: [Freesurfer] registering to fsaverage

Trisanna, has this issue been resolved? doug On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote: > Hi Bruce > > here is the output of my mri_vol2surf for a volumetric spam created in > minc tools. When I then overlay this result in Freeview, it displays a > Min of 127 and a Max of 255. > >

Re: [Freesurfer] convert from MNI152 to native space

Is this problem resolved? There is a new version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg On 06/16/2016 11:05 AM, Leila Reddy wrote: > Hi FS Experts, > > I'm trying to use the mni152reg command but I get an error that --lta > is not recognized. > > It appears

Re: [Freesurfer] Intensity stats question

On 07/06/2016 01:05 PM, Sabrina Yu wrote: > > Hello, > > > I have a couple of questions about the wmparc.stats file generated. > What volume is the data based on? > norm.mgz > > Has the intensity of the volume been corrected? > Yes > > I just need the average voxel intensity over the ROIs, but

Re: [Freesurfer] mris_preproc subject-volume mismatch

can you send the terminal output? On 07/06/2016 11:32 AM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I'm trying to use mri-preproc to do a group fMRI analysis(based on the > tutorial). However, I keep getting an error that the number of input volumes > does not equal number of subjects. It

Re: [Freesurfer] question about white matter edits

Hi Rito, I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel value less than 110)."

[Freesurfer] Intensity stats question

Hello, I have a couple of questions about the wmparc.stats file generated. What volume is the data based on? Has the intensity of the volume been corrected? I just need the average voxel intensity over the ROIs, but am unsure if this intensity is based on an intensity normalized brain volume.

[Freesurfer] TRACULA tract group comparison p-values

Dear Freesurfers, I am looking for a way to add a colorbar to my p-value tract cores generated through TRACULA. When I load up the images as described in the tutorial here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I only get a colorbar from 0 to 28.5 which cannot

[Freesurfer] mris_preproc subject-volume mismatch

Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to

Re: [Freesurfer] hippocampal subfields command

Thanks. Only for FS 6.0 and later, correct? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias, Eugenio Sent: Wednesday, July 06, 2016 9:47 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Not yet, sorry. But it’s on my todo list. Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at 14:39, Hibert, Matthew Louis > wrote: Hi

Re: [Freesurfer] hippocampal subfields command

Hi Jim, the latter command uses a new, higher resolution atlas based on ex vivo scans. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios

[Freesurfer] hippocampal subfields command

A quick question re: hippocampal segmentation. I have processed 1mm isotropic T1 data with 5.3 using the following command: recon-all -qcache -all -hippo-subfields How is this this different than using the following command I have found here:

Re: [Freesurfer] segmentation issues in Temporal Lobes

Dear Bruce, Thanks a lot for clarifying. Best wishes, Barbara On 06/07/2016 15:57, Bruce Fischl wrote: > Hi Barbara > > yes, this is intentional and shouldn't be a problem. The hippocampus has > lots of internal structure that we don't model with the surfaces (but we do > with the subfield

Re: [Freesurfer] Inquiries about the curvature

Hi Mahtab you should look them up in a differential geometry textbook. Essentially, a 2D surface has two curvatures at each point, one in the direction of maximum folding (k1) and one in the direction of minimum folding (k2). The Gaussian curvature is then k1*k2 and the mean is (k1+k2)/2

Re: [Freesurfer] FSFAST time series extraction

Hi Doug, Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from Buckner 2011 7 Cerebellar network. Please see below for the steps I performed to extract time series from Buckner 2011 7 Cerebellar networks. If you could give your thoughts on the steps/process that'd be great.

Re: [Freesurfer] segmentation issues in Temporal Lobes

Hi Barbara yes, this is intentional and shouldn't be a problem. The hippocampus has lots of internal structure that we don't model with the surfaces (but we do with the subfield stuff), but we exclude it from our analyses so you should be fine cheers Bruce On Wed, 6 Jul 2016, Barbara

Re: [Freesurfer] Freesurfer/Freeview help

Hi Abbie you might check out Matti Hamalainen's MNE software. He does both boundary and finite element analysis. We distribute a test subject named "bert" you can use cheers Bruce On Tue, 5 Jul 2016, Abbie McNulty wrote: Hello, Just a couple more questions that would be great if you could

Re: [Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

See if this page helps http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats On 7/6/16 9:07 AM, Kaiming Yin wrote: Dear experts, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles

Re: [Freesurfer] segmentation issues in Temporal Lobes

Hi, There is nothing to solve — that is the expected behavior around the hippocampus/amygdala. See this FAQ: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt hestructuresthere.HowcanIfixthis.3F

Re: [Freesurfer] mri_surfcluster

use this program ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr On 7/6/16 9:22 AM, tom parker wrote: Dear Freesurfers, I ran a comparison between different groups using mri_glmfit. Now I would like to correct the results in sig.mgh by multiple comparisons using FDR.

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Have you had a chance to look into the possibility of combining the -hires flag with the hippocampal subfield segmentation? Thanks, Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias,

[Freesurfer] mri_surfcluster

Dear Freesurfers, I ran a comparison between different groups using mri_glmfit. Now I would like to correct the results in sig.mgh by multiple comparisons using FDR. I tried using tksurfer but it doesn't work so well on my computer and I read that freeview does not allow to do that yet. I'm now

[Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

Dear experts, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit

[Freesurfer] Inquiries about the curvature

Dear FreeSurfer, I am using the mris_anatomical_stats output to calculate the curvature and thickness indices for different brain areas. However, I am not sure what the mean and gaussian curvatures mean. I could not find a complete description on these two. Would you please guide me what

Re: [Freesurfer] Hippocampal Subfields Segmentation

Dear all, We are working on this; I'll write again when the problem is solved (hopefully soon!) Cheers Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: