Re: [Freesurfer] TRACULA ERROR!!

What do you see when you run: ls /media/brain/brains/TN_retro/Tracula/AN01/mri From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lin, Yizhi [l...@union.edu] Sent: Monday, August 07, 2017 3:22 PM To: Freesurfer

Re: [Freesurfer] tracula problem

Hi Ariel – Have you run freesurfer on the structural images of your subjects? Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in your configuration file? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

Can anyone provide me the link of freesurfer version 5.3 vdi file? I was trying to install it in windows 10 using virtual box, but its not working. Thanks Ruchira From: Tabassum, Ruchira Sent: Saturday, August 5, 2017 1:22 PM To: 'freesurfer@nmr.mgh.harvard.edu'

Re: [Freesurfer] pineal gland

Hi Rotem, can you repost with previous correspondence? On 08/07/2017 02:59 PM, Rotem Saar wrote: > Dear Bruce and Doug, > > Thank u for your replay saying that it is possible to manually draw > the pineal gland using freeview and extract stats for it. > > Can u please refer me to a link on

Re: [Freesurfer] Cortical thickness map for a pediatric case

Hi Bruce, Sure, please see highlighted below part of screen output showing the error. Since I ran the command within a screen sesison I have saved executed screen session to a log file. Find attached log file with output of entire run. Please let me know if any other files are required and if

Re: [Freesurfer] mri_glmfit-sim output

see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > In the mri_glmfit-sim summary output file, I get a number of output > variables, and I'm not sure what some of them are.

Re: [Freesurfer] TRACULA ERROR!!

Hi Ariel – Have you run freesurfer on the structural images of your subjects? Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in your configuration file? Best, a.y From: > on

[Freesurfer] mri_glmfit-sim output

Dear Freesurfer team, In the mri_glmfit-sim summary output file, I get a number of output variables, and I'm not sure what some of them are. Could you explain the ones in bold to me? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLow CWPH NVtxsWghtVtx

[Freesurfer] pineal gland

Dear Bruce and Doug, Thank u for your replay saying that it is possible to manually draw the pineal gland using freeview and extract stats for it. Can u please refer me to a link on wiki that explain how to do it? I'm not familiar with this procedure and although Doug explain it in brief I feel

[Freesurfer] postdoc ad

Please, see attached or below for details. Lilla Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla Zöllei A postdoctoral fellow is recruited for an NIH funded project for developing

Re: [Freesurfer] Pial surface editing

Hi, After checking the images in the viewer, it appears that 001.mgz and brainmask.mgz are in the correct orientation, but brain.mgz (created by freesurfer) is rotated 90 degrees. The dimensions of the images don't match either. 001.mgz and brainmask.mgz are: dim1 219 dim2

Re: [Freesurfer] Updating FreeSurfer v5.1 statistics to FreeSurfer v5.3

I can't remember all the differences:), but there might have been a change in how the estimated ICV is computed, and the partial volume correction may have changed. I general, I think it should be fine On 08/07/2017 01:23 PM, Hatton, Sean wrote: > Hello FreeSurfer experts, > > I have many

Re: [Freesurfer] Updating FreeSurfer v5.1 statistics to FreeSurfer v5.3

Thank you for your reply, that is all I am seeing :D Have a great week! Sean Hatton, PhD Postdoctoral Scholar, Department of Psychiatry UCSD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] TRACULA ERROR!!

Dear Anastasia, I used dicom images to run my subjects, and yes, those freesurfer recons were found in SUBJECTS_DIR in my configuration file. Thanks. best, Ariel On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia wrote: > Hi Ariel – Have you run freesurfer on the

[Freesurfer] tracula problem

I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC

Re: [Freesurfer] Pial surface editing

what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce,  Here is what I did. For each subject: a) used the original (non-skull stripped) brain

Re: [Freesurfer] Thalamus ROI

Thank you so much. That was really helpful. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, August 07, 2017 7:15 AM To: Freesurfer support list

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

=== server2:20170214_JEL JuhyoungRyu$ recon-all -subject JEL_v6 -i T1_bfc.nii -T2 T2_bfc.nii -T2pial -all -hires INFO: hi-res volumes are conformed to the min voxel size Subject Stamp:

Re: [Freesurfer] Pial surface editing

what viewer did you check in? If not freeview, look at it in freeview On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi,  After checking the images in the viewer, it appears that 001.mgz and brainmask.mgz are in the correct orientation, but brain.mgz (created by freesurfer) is rotated 90

Re: [Freesurfer] Cortical thickness map for a pediatric case

thanks Sneha you'll probably need to wait until tomorrow for Martin to read his email :) cheers Bruce On Mon, 7 Aug 2017, Sneha Pandya wrote: Hi Bruce, Sure, please see highlighted below part of screen output showing the error. Since I ran the command within a screen sesison I have saved

[Freesurfer] Extracting pial surface from manually pareclated atlas

Hi freesurfer team I'm just wondering if there is any way to extract left and right pial from manually parecllated file apar+aseg .mgh I need to view them with the new parecellation file Thanks in advance Fatima ___ Freesurfer mailing list

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

Hi Juhyoung can you just cut and paste the text into the email instead of a screen shot? thanks Bruce On Mon, 7 Aug 2017, Juhyoung Ryu wrote: Sure, screenshot image is below with commands. On Aug 7, 2017, at 11:14 AM, Bruce Fischl wrote: can you send us

Re: [Freesurfer] Thalamus ROI

Hi Sara sure, you can look up the thalamus labels in FreeSurferColorLUT.txt (10 and 49 for lh and rh), then use either mri_extract_labels or mri_binarize to pull our ROIs. cheers Bruce On Mon, 7 Aug 2017, sarai...@alumni.ubc.ca wrote: > Hi Freesurfer team, > Is it possible to extract Thalamus

Re: [Freesurfer] installtation error

try SetUpFreeSurfer.sh (note the capital letters) On 8/5/17 11:04 PM, 水墨丹青 wrote: TO: freesurfer@nmr.mgh.harvard.edu FROM: fsu...@worlduniversity.edu SUBJECT: installation error error: there is no setupfreesurfer.sh file Hello FreeSurfer Developers, I'm attempting to install freesufer on

[Freesurfer] Cortical thickness map for a pediatric case

Dear team, I have completed cross-sectional pipeline on my pediatric case with a baseline and 4 follow up time points between 4-7 years of age. However, I was not able to run longitudinal pipeline on it as the base template creation failed with some topological errors. I assume this failure

Re: [Freesurfer] susceptibility-induced distortions

Hi John I think the FSL group has some nice tools to fix these distortions either with or without field maps (topup for example) cheers Bruce On Mon, 7 Aug 2017, John Anderson wrote: Dear Freesurfer experts, I want to inquire if there are any tools or any methods to improve T1 images

[Freesurfer] Updating FreeSurfer v5.1 statistics to FreeSurfer v5.3

Hello FreeSurfer experts, I have many FS5.1 edited-subjects that I want to use in an application that only takes FS5.3 formatted statistics. I ran 20 subjects in FS51 and FS53. I took the FS51 subjects and reran recon-all -segstats (in FS53) and it updated aseg.stats closer to the values for

[Freesurfer] Sampling vertex-wise data across various distances from the core of a mask to a somewhere else on fsaverage

Hi Doug and Freesurfer Experts, I am trying to see whether cortical thinning gets progressively less severe as we move further away from a seed/voxel (e.g. precuneus). Is it possible to perform correlations between the (a) distance between a given vertex to specific point on fsaverage, and the

Re: [Freesurfer] susceptibility-induced distortions

it should, although you may need to configure it differently since the distortion is in a different direction. We have used it to correct FLASH readouts cheers Bruce On Mon, 7 Aug 2017, John Anderson wrote: Dear Dr Bruce, Thank you very much for the quick response. Topup works for DTI

Re: [Freesurfer] Cortical thickness map for a pediatric case

Hi Sneha can you include the output as text instead of an image? thanks Bruce On Mon, 7 Aug 2017, Sneha Pandya wrote: Hi Bruce, Please find attached recon-all.log file and I used following command to run the base: recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3

Re: [Freesurfer] susceptibility-induced distortions

Dear Dr Bruce, Thank you very much for the quick response. Topup works for DTI and I am wondering if it works for the T1 images. Thanks again! John > Original Message > Subject: Re: [Freesurfer] susceptibility-induced distortions > Local Time: August 7, 2017 1:54 PM > UTC Time: