Re: [Freesurfer] subcortical segment NIFTI files

Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: > Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. > > I am able to obtain, for example, the right amygdala, using the following > commands: > >

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

you have specified the hemi as lh but passed it the rh thickness On 6/16/14 8:44 AM, kangchengwang0...@gmail.com wrote: Dear Bruce, Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structura

Re: [Freesurfer] Questions about cluster-wise correction

On 6/15/14 2:24 PM, wangzhiwei3233 wrote: Hi, all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections for one same result,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 *abs* --cwpvalthresh .05 --2spaces b. mri_glmfit-

Re: [Freesurfer] Fwd: Extracting mean diffusivity values from diffusion data in freesurfer 5.3

I don't think that MD values have to be between 0 and 1. Try looking at a larger white matter structure to see if it is more reliable. Also check your mask. On 6/11/14 7:11 PM, Rotem Saar wrote: Dear freesurfer experts, I'm using freesurfer 5.3 for extracting FA and MD values for each reg

Re: [Freesurfer] Get thickness of one peak vertex for a group subject

You can use mri_segstats with the --vox option. Spec --vox vertexno 0 0 and the thickness file as the --i On 6/10/14 1:16 PM, Xiangzhen Kong wrote: Hi, all. Is there any FS tool for extracting the thickness value of a peak vertex ? From glmfit, I have got the vertex index of the peak. Thanks

Re: [Freesurfer] mri_glmfit for longitudinal 3 group analyses

The y.mgh file is the "stack" of inputs (ie, each frame is a different map). In your case, assuming you want to do a thickness study, you would run mris_preproc and use the --fsgd option and specify --meas thickness (and set the other needed options), and mris_preproc will produce a stack for

Re: [Freesurfer] Displaying subset of labels on template

You can also recombine the labels into an annotation with mris_label2annot doug On 6/11/14 9:15 PM, dgw wrote: You could use mri_annotation2label Then just load only the labels you care about. HTH D On Wed, Jun 11, 2014 at 3:11 PM, nmw > wrote: Greetings

Re: [Freesurfer] Error Covarying for Gender

Try demeaning the continuous variables. By this I mean to compute the mean of the age across all subjects regardless of group, then subtract this mean from the age of each individual. doug On 6/10/14 10:00 PM, Thomas DeRamus wrote: Sorry to be a bother, but I seem to be having an issue with

Re: [Freesurfer] Messages not appearing on Mail Archive

Hi Sherryse, sorry for the delay, I've been traveling. I think the problem may be with your version of reg-feat2anat. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Copy that into $FREESURFER_HOME/bin (after making a backup of the one

Re: [Freesurfer] Fw: Problem with uploading Cluster Simulation data

You should be able to view the map results in freeview just as you would any other map. doug On 6/12/14 12:19 PM, car...@van-vlodrop.de wrote: *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr *Von:* "car...@van-vlodrop.de" *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Problem with upl

Re: [Freesurfer] volume-based controls

what kind of volume-based analysis? You can get volumes of ROI structures from FS, and FSFAST allows you to do map-based analysis of fMRI for subcortical structures in the volume. Otherwise, you might try using VBM doug On 6/12/14 11:21 PM, kristen yoo wrote: > I am attempting to do volume-b

Re: [Freesurfer] subcortical segment NIFTI files

It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol

Re: [Freesurfer] subcortical segment NIFTI files

Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Y

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

Hi Wang you can't change the atlas that way. We extract a ton of information and store it in what we call an atlas, and what we require isn't in the harvard-oxford one. What are you trying to achieve? cheers Bruce On Mon, 16 Jun 2014, kangchengwang0...@gmail.com wrote: Dear Bruce, Now,

[Freesurfer] smoothing functional data on smoothwm surface

Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer f

Re: [Freesurfer] subcortical segment NIFTI files

Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the rig

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

Dear Bruce, I try to extract freesurfer cortical thickness valunes for a ROI defined in volume space (avg152T1.nii.gz). I try a lot and have extracted the values successfully now. Thank you very much. I suggest the experts can change opition "--reshape" of mri_vol2surf and mri_surf2surf into

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

Dear Douglas Greve, Thank you very much. I change it and change the option of reshape into noreshape. Then, it could be sucessful. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] question on summary file from monte carlo simulation

Dear Freesurfers, When I do the Monte-Carlo simulation after mri_glmfit between my groups, I get an output summary file for each of my contrast. In that summary file, there are multiple columns for coordinates, threshold values, number of vertices and size (mm2). My question is, how

Re: [Freesurfer] question on summary file from monte carlo simulation

It is computed from the area of the triangles in the cluster. Actually, it is computed from the mean area over the group used to create fsaverage. Not sure what you mean by a standard algorithm doug On 6/16/14 4:34 PM, Govindarajan, Koushik Athreya wrote: Dear Freesurfers, Wh

Re: [Freesurfer] mri_segstats

On 6/9/14 7:10 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi, > I have two questions about mri_segstats. I want to measure the surface > area of a functionally-defined ROI. I used the mri_segstats as below > and I want to be sure that it is correct. Please note that ROIs were > defined in the

Re: [Freesurfer] epidewarp.fsl

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl doug On 6/10/14 4:14 AM, XJ Kang wrote: > Hi again, > > I posted a question about the script "epidewarp.fsl" but didn't see the > answer. Anybody know where I can find a version working under fsl-5.X? > Than

Re: [Freesurfer] Fwd: How to extract significant result for each subject

mri_surfrft_jlbr does not output that kind of information. I'd have to modify it. I'm traveling now. Can you check back in two weeks? doug On 6/13/14 9:17 AM, kangchengwang0...@gmail.com wrote: Hi dr Jerome J Maller The analysis I do this research was followed as th_e tutorials

Re: [Freesurfer] smoothing functional data on smoothwm surface

Use mri_surf2surf with the --fwhm option doug On 6/16/14 3:13 PM, Milde, Christopher wrote: Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I

Re: [Freesurfer] subcortical segment NIFTI files

That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain Free

[Freesurfer] registration of functional data to inflated brain

Hi Douglas, This worked. Thank you so much! Just in the knick of time as the presentation is Wednesday! For anyone having issues of reg-feat2anat not producing register.dat or anat2exf.register.dat . . . The link below should solve your problem! Best, Sherryse Message: 19 Date: Mon, 16 Jun

Re: [Freesurfer] subcortical segment NIFTI files

Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --m

Re: [Freesurfer] subcortical segment NIFTI files

sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right

Re: [Freesurfer] Vol stats of precentral gyrus

I don't know whether this was answered or not, but the precentral gyrus would not be reported in the subcortical volume stats. If you want to know the rules used to draw precentral, then I refer you to the paper by Desikan, et al, that describe the process. doug On 6/10/14 10:21 AM, Hugh Pem

[Freesurfer] Number of Slices

Hi, I want to perform recon-all on four different structural sequences for the same participant. Three of the sequences have the same number of slices, whereas the T1 has fewer slices, so when I input the different sequences with the recon-all command, I get the following error: ERROR: inputs have

Re: [Freesurfer] Number of Slices

Hi Caroline do you want to pocess each one independently, or are you hoping to motion correct and average them for just one processing? If the latter, you probably don't want to do it if the sequences are substantially different. cheers Bruce On Mon, 16 Jun 2014, Caroline Lewis wrote: > Hi

[Freesurfer] Using QDEC for 3 groups x 2 time-points

Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of the two-stage model, and I would prefer to run stage#2 (cross-sectional analysis of the di

Re: [Freesurfer] Number of Slices

Hi Bruce, I was hoping to just do one processing, but perhaps as you suggest that's not the best idea (the T1 has 136 slices whereas the other sequences have 48). I have acquired these sequences to identify lesions in some participants and am trying to figure out how to register/align the other 3

Re: [Freesurfer] Number of Slices

Hi Caroline what are the scans? If they have only 48 slices you almost certainly don't want to run them through recon-all. Probably you just want to run the 136 slice sequence and go from there. Bruce On Mon, 16 Jun 2014, Caroline Lewis wrote: > Hi Bruce, > > I was hoping to just do one proce

Re: [Freesurfer] Number of Slices

Hi Bruce, There's a pdt2, flair and gre. If I just run recon-all on the T1, is there a way to register these other sequences to the T1? Thanks, Caroline On Mon, Jun 16, 2014 at 2:41 PM, Bruce Fischl wrote: > Hi Caroline > > what are the scans? If they have only 48 slices you almost certainly

Re: [Freesurfer] Number of Slices

Hi Caroline yes, you can use bbregister to register them to the surfaces derived from the T1 (which in general is more accurate than registering directly to the T1) cheers Bruce On Mon, 16 Jun 2014, Caroline Lewis wrote: Hi Bruce, There's a pdt2, flair and gre. If I just run recon-all on t

Re: [Freesurfer] Linear Mixed Models in FS‏

Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age (might be a random effect too) +  Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(rand

Re: [Freesurfer] pial edits near cerebellum and problems in sagittal view

Elisa and Stephanie, This is an unusual variant of Elisa's name. "Elissa" I have not seen that before, Brad From: Elissa McIntosh [mcintosh.eli...@gmail.com] Sent: Monday, June 16, 2014 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

Yes, you could do each separately. doug On 6/16/14 8:10 PM, Tudor Popescu wrote: Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of th

Re: [Freesurfer] template registration and wm edits

Hey Bruce, I'm referring to the MNI305 which freesurfer uses for linear registration. I know this is an adult template, and I wanted to try and use an NIH atlas designed from 2-5 year olds (same age as my subjects). I was interested in seeing if I get different results from the MNI305. As fo

[Freesurfer] Announcing PySurfer version 0.5

Hello everyone, We are pleased to announce the release of PySurfer version 0.5. PySurfer is a Python library for making beautiful and reproducible visualizations of Freesurfer data. Changes in this version include - The statistical overlay functions can now use a wi

[Freesurfer] Group analysis over different studies?

Hi all, I want to do a group analysis using subjects that were run in different studies but who have (some of) the same relevant functional contrasts. Is there a way to run something like isxconcat-sess on data from different analysis streams? Or if not, which files do I need to collect and align

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

Hi Doug, Thanks... Presumably I'd just leave each possible pair of groups at a time in the qdec table, and delete rows corresponding to subjects of the remaining group? And then do stats on, e.g. "long.thickness-rate" to compare rate of change between the current pair of groups? Doesn't variabilit

[Freesurfer] CSF volume

Hi FS community, I was wondering whether there is a way to calculate accurately the CSF volume with FreeSurfer (I have both T1 and T2 images). Should I just add the ventricular structures and the CSF volume reported in aseg.stats or is there another way to account for the sulcal CSF based on the T

Re: [Freesurfer] CSF volume

Hi Panos sorry, we don't segment sulcal CSF Bruce On Mon, 16 Jun 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS community, > > I was wondering whether there is a way to calculate accurately the CSF > volume with FreeSurfer (I have both T1 and T2 images). Should I just add > the ventricular st

Re: [Freesurfer] template registration and wm edits

Hi Matt yes, you need to set them to 1 I believe, not 0. The most recent version of freeview has a "recon edit" mode, which will do this automatically. As far as using your own template, that should be pretty straightforward. Hopefully either Nick or Avi can let you know how cheers Bruce On M

Re: [Freesurfer] subcortical segment NIFTI files

Hi Doug, I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then? Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? Thanks! Daniel From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mg

Re: [Freesurfer] pial edits near cerebellum and problems in sagittal view

Hi Elissa It's certainly grabbing a bit of the tentorium, but not much. The rest is hard to assess. Try looking in a coronal view at some of the ambiguous regions Cheers Bruce > On Jun 16, 2014, at 3:22 PM, Elissa McIntosh > wrote: > > Hi, I'm new to manual editing and I'm noticing some pote

[Freesurfer] problem of Label file

Hi all, I create a label file according to my result using QDEC, does it correct? why some number is so large? #!ascii label , from subject vox2ras=TkReg 260 963 -9.181 41.343 -47.222 0.00 1515 -9.022 44.425 -43.083 0.00 1516 -7.070 45.386 -46.312 0.00 3485 -