[Freesurfer] slice timing correction fmcstc files are lacking

Hi list, I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.I have acquired data using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder siemens"?The command line:preproc-sess -s Sess201 -fwhm 5 -surf

Re: [Freesurfer] Trakula

Hi Anastasia, Thank you very much for your help and recommendations. I will try to fix These Problems. I would like to ask you one more question. Is there any command which could help me to invert the gradient vectors for my DWI scan in the z direction? Best Bahram 2015-08-24 17:57 GMT+02:00 Anast

[Freesurfer] Create matrix

Hi Doug, I am using the command "mri_volsynth" to create voxel has specific dimensions and position in the brain. Kindly, I would like to inquire if there is any tool in Freesurfer that can help to create volumetric matrix has a number of columns and rows ( and as a results number of voxels) l

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

it would fix the hippocampal problems and maybe the cortical ones as well cheers Bruce On Tue, 25 Aug 2015, fmri wrote: > I have already processed 88 subjects in this version, > > would it matter if I process or re-process subjects with another version? > > > On Aug 25, 2015, at 3:44 PM, Bruce F

Re: [Freesurfer] Create matrix

does mri_volsynth not work for this? On 8/26/15 9:25 AM, Alshikho, Mohamad J. wrote: Hi Doug, I am using the command “mri_volsynth” to create voxel has specific dimensions and position in the brain. Kindly, I would like to inquire if there is any tool in Freesurfer that can help to create

Re: [Freesurfer] Trakula

Hi Bahram - The gradient table is a text file with 3 columns. You need to multiply the 3rd column by -1. You can do this in matlab, awk, perl, or any scripting language that handles text files. Best, a.y On Wed, 26 Aug 2015, B M wrote: Hi Anastasia, Thank you very much for your help and re

Re: [Freesurfer] Create matrix

Hi Doug, I am using the following command line to create single voxel has the same dimensions and position ( from single voxel (svs) MRS data): mri_volsynth --vol BS.nii --pdf const --dim 40 40 40 1 --res 0.5 0.5 0.5 1 --cdircos 0.025458 -0.999671 0.003154 --rdircos -0.670601 -0.014738 0.741673

Re: [Freesurfer] Create matrix

No pic attached. That command will create a volume with 40 voxels on a side and FoV of 20mm. What more do you want? On 8/26/15 10:26 AM, Alshikho, Mohamad J. wrote: > Hi Doug, > I am using the following command line to create single voxel has the same > dimensions and position ( from single voxe

[Freesurfer] Error running recon-all -localGI

Hi Freesurfer Support, I posted this question about a month ago, and I still haven't found a solution. Any help would be greatly appreciated. When running the recon-all -localGI command, I get the following errors, which result in the message: make_roi_paths did not complete successfully! Er

[Freesurfer] making ROI after bbregister

Dear all experts, I am currently dividing the gray matter into 6 different layers using bbregister, however, does anyone know how to make the space between layers into ROIs? Thanks! Appreciating your idea. Yun ___ Freesurfer mailing list Freesur

Re: [Freesurfer] Error running recon-all -localGI

Hi Philip, Can you send me the full recon-all.log for this subject so that I can see also matlab version and whether other vertices ran or if it crashed on the first one. Thanks, Marie On Aug 26, 2015, at 8:00 AM, Philip Deming mailto:pdem...@wisc.edu>> wrote: Hi Freesurfer Support, I pos

Re: [Freesurfer] Create matrix

So do you need anything else? On 8/26/15 10:51 AM, Alshikho, Mohamad J. wrote: I attached the photo. Actually I didn't realize that this FOV 20 will be consisted of 40 voxels because when I view the output of the previous command line this will look like one big volume!

Re: [Freesurfer] making ROI after bbregister

I'm not sure what you mean. bbregister does not divide gm into layers. Can you elaborate on what you have done and trying to do? On 8/26/15 11:02 AM, Yun Wang wrote: > Dear all experts, > > > I am currently dividing the gray matter into 6 different layers using > bbregister, however, does anyone

Re: [Freesurfer] making ROI after bbregister

we have toold for doing this but they aren't documented (mris_expand, mri_compute_layer_fractions, mris_compute_layer_intensities). This is what Rebecca Shafee used in her recent two-compartment paper http://www.ncbi.nlm.nih.gov/pubmed/25449739 cheers Bruce On Wed, 26 Aug 2015, Douglas Greve

Re: [Freesurfer] Create matrix

Thanks a lot a Doug! From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, August 26, 2015 11:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] Create matrix So do you need anything else? On 8/26/15 10:

[Freesurfer] extract values of individual cluster‏

Dear FS experts,Reposting my message below.Thanks I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is

Re: [Freesurfer] making ROI after bbregister

Usage: mri_compute_layer_fractions [options] What is ? ? > On Aug 26, 2015, at 10:37, Bruce Fischl wrote: > > we have toold for doing this but they aren't documented (mris_expand, > mri_compute_layer_fractions, mris_compute_layer_intensities). This is what > Rebecca Shafee used in her r

Re: [Freesurfer] making ROI after bbregister

it is the registration between and the surfaces/conformed volumes. If you are just using the volumes used for recon then it can be identity.nofile cheers Bruce On Wed, 26 Aug 2015, Yun Wang wrote: Usage: mri_compute_layer_fractions [options] What is ? ?  On Aug 26, 2015, at 10:3

[Freesurfer] subcortical segmentation of thalamic nuclei

Dear Freesurfers, Is it possible to segment using freesurfer specific thalamic nuclei, for example, the VPL? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] how to fix errors in 3d mesh

Hi all, I am an interested neuroscience newbie and I am following this excellent online guide on how to create a 3d print of my cortex using an MRI scan and freesurfer: http://nmarinsek.com/3D-printed-brain/ Sofar, i have been successful in generating t

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

what version should I try? On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote: > it would fix the hippocampal problems and maybe the cortical ones as well > > cheers > Bruce > On > Tue, 25 Aug 2015, fmri wrote: > >> I have already processed 88 subjects in this version, >> >> would it matter if

Re: [Freesurfer] subcortical segmentation of thalamic nuclei

Hi Emma not yet, sorry Bruce On Wed, 26 Aug 2015, Emma Thompson wrote: > Dear Freesurfers, > Is it possible to segment using freesurfer specific thalamic nuclei, for > example, the VPL? > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] how to fix errors in 3d mesh

Sounds like you had a clinical scan and got a copy of a sagittal scan series and an axial scan series.  Those would be "2D" acquisitions in which the slice thickness is probably considerably thicker than the in-plane resolution.  That kind of data isn't ideal for FS.  Rather, data for FS is

Re: [Freesurfer] how to fix errors in 3d mesh

Hi Alexander I doubt it actually has a whole. We have automated topology correction that prevents this. You can use mris_euler_number to check. I am a bit surprised that you only have 30-something images. That is typically not nearly enough to cover the brain at high-enough resolution for go

Re: [Freesurfer] Error running recon-all -localGI

Thanks for the quick response, Marie. Here's the full recon-all.log for this subject: FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer-latest Actual FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer_5.10_x86_64 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 L

[Freesurfer] freeview read error

Dear Experts, I am trying to use Freeview to view volumes using the command listed on the website:  http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that loads is the aseg.  I am not able to load the T1, wm, or brainmask mgz’s . either from the terminal or through

Re: [Freesurfer] freeview read error

Hi Cat do those file exist? What does ls -l tell you for them? Bruce On Wed, 26 Aug 2015, Cat Chong wrote: Dear Experts,   I am trying to use Freeview to view volumes using the command listed on the website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that l

Re: [Freesurfer] Error running recon-all -localGI

Hi Philip, It seems that for a strange reason your ROIs are not getting saved. I never saw this one. I suppose that you are getting this error for all subjects? Do you have a way to transfer me one of your subject so that I can have a closer look? Thanks, Marie On Aug 26, 2015, at 11:37 AM,

Re: [Freesurfer] freeview read error

Hi Bruce, Yes, they exist.but this seems strange...-rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx MF\Domain Users         0 Aug 26 09:12 brainmask.mgz On Wednesday, August 26, 2015 12:04 P

Re: [Freesurfer] freeview read error

they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong wrote: Hi Bruce, Yes, they exist. but this seems strange... -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx

Re: [Freesurfer] how to fix errors in 3d mesh

Thanks Bruce. Yes, I was honestly also a bit surprised I only had 32 images in one scan. See my reply to Michael, I basically went looking for a place where I could get a general MRI scan which I could pay out-of-pocket. I guess I should keep looking to get a better 3D MRI scan. I will have a

Re: [Freesurfer] freeview read error

no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl wrote: they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong wrote: > Hi Bruce, > > Yes, they exist. > but this seems strange... > -rwx--+ 1 mxx  MF\Doma

Re: [Freesurfer] how to fix errors in 3d mesh

Thanks Michael. Yes, it was a clinical scan. I basically went looking for a place to get an MRI scan which I could pay for out-of-pocket. I told them it was for my personal interest, in particular to create a 3d model, but I hadn’t found the freesurfer guideline by then yet, so I couldnt exact

Re: [Freesurfer] freeview read error

did you run recon-all? If so, check the recon-all.log for errors On Wed, 26 Aug 2015, Cat Chong wrote: no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl wrote: they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong

Re: [Freesurfer] how to fix errors in 3d mesh

Typically we use an mprage with 1mm isotropic resolution, but depending on your coil/field strength you might want it to be a bit lower res to improve CNR (say 1.1mm isotropic,which as 20% more SNR than 1mm) On Wed, 26 Aug 2015, Alexander van Dijk wrote: Thanks Michael. Yes, it was a clin

Re: [Freesurfer] how to fix errors in 3d mesh

Ok thanks, i’ll keep looking for a better scan. I was already very happily surprised with how the 3d mesh for my left hemisphere came out with my 32-image T1 scan. > On Aug 26, 2015, at 12:36 PM, Bruce Fischl wrote: > > Typically we use an mprage with 1mm isotropic resolution, but depending o

Re: [Freesurfer] TRACULA and eddy (FSL)

Dear Anastasia, Thank you very much for the quick help. Best wishes, Barbara Anne On 25/08/2015 22:10, Anastasia Yendiki wrote: > Hi Barbara - Yes, just correct with the method of your choice, apply the > rotation to the gradient vectors, pass the corrected images and gradient > vectors to tracu

[Freesurfer] Automatic Subcortical Segmentation Editing?

Hello All, I am hoping to make some edits to subcortical segmentations, and while I have found instructions for manual edits, there are also stern warnings to avoid these if possible and pursue automated avenues. I cannot, however, seem to find clear instructions on how to automatically edit t