Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

AM To: Freesurfer support list Cc: Douglas Merkitch Subject: Re: [Freesurfer] Longitudinal stream finalsurfs misalignment? Hi Doug, probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-

[Freesurfer] Longitudinal stream finalsurfs misalignment?

913.tar' via the filedrop website. Any help would be appreciated! Thanks, Doug Douglas Merkitch Clinical Research Coordinator 355 E. Erie St, Chicago, IL 60611 312-238-5911 office dmerki...@sralab.org [cid:image002.jpg@01D56A28.22DB2140] sralab.org<http://www.sralab.org/> Face

Re: [Freesurfer] Segmenting the Corpus Callosum

Hey Bruce, Could you elaborate on what steps you would need to change the number of corpus callosum segments (and grow them laterally), and how to specify the outputs name/format/location? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center On Feb 19, 2018

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

The same thing happened to me on my mac when I changed the FREESURFER_HOME variable in the terminal, but not in the .bashrc file that I source when the terminal opens. Hope this helps! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center On Feb 9, 2017, at 1

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

olume.mgz \ --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \ --inv \ --mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \ --o lowb.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg Thanks again for the help! Thanks, Doug Douglas Merkitch Neurological Scie

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

t the results were not great so I suspect that something is incorrect in the syntax and/or inputs. Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center On Jan 26, 2017, at 2:41 PM, Douglas Merkitch mailto:douglas_merki...@rush.edu>> wrote: Hello Lilla, Tha

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

for your help! Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Jan 26, 2017, at 8:42 AM, Lilla Zollei mailto:lzol...@nmr.mgh.harvard.edu>> wrote: Hi Doug, In order to compute a

[Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

t back to subject diffusion space? Is this possible? If so, what would that command look like and what other steps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:doug

Re: [Freesurfer] TRACULA - RH ILF Issue

___ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Douglas Merkitch [douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu>] Sent: Thursda

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

suggests to me that it's not a permissions issue? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Nov 29, 2016, at 4:15 PM, D

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

: Expression Syntax. === I did a quick search of the mail archives involving Mac and dyld variables, and it seems like this may be something that you may provide a fix for? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

response and I apologize for my error. Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Nov 29, 2016, at 3:20 PM, Douglas Merkitch mailto:douglas

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

ompt response! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Nov 29, 2016, at 3:12 PM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: can you send your comma

[Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

6-beta-20161116-5037eae on a Mac Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5. Any help would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu<mailto:douglas

[Freesurfer] Freeview -dti Display as Vectors Discrepancy

freeview from freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae. Is this a known issue with a patch available? Any insight would be greatly appreciated. Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email

[Freesurfer] Older Freesurfer Version with Freesurfer v. 6 HSF & Brainstem Modules

new v. 6 HSF and brainstem modules? 2) Our data was acquired using a 1.5 T scanner (~1mm isotropic). Would this be an issue for either the new v. 6 HSF or brainstem modules? Any answers and/or comments as to your thought process behind your response would be appreciated! Thanks, Doug Douglas

[Freesurfer] Two Different T1 Acquisition Planes as recon-all Inputs

y insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> ___ Fr

[Freesurfer] Hippocampal Subfields on 1.5 Tesla - Freesufer v. 6

wrong!). Would the same apply for the new HSF module in Freesurfer v. 6 when it is officially released? Any insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.

Re: [Freesurfer] TRACULA preprocessing error

Hello D, Thanks for the advice! Your suggestion did the trick! I remember reading about properly formatting the bval/bvec files, but I apparently forgot to do so... Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660

Re: [Freesurfer] TRACULA preprocessing error

Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Nov 9, 2015, at 6:39 AM, denizzgursel mailto:denizzgur...@gmail.com>> wrote: Dear all, I am running Tracula preprocessing on N

[Freesurfer] Tracula Processing Question

data)? Any advice or insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> ___ Freesurfer mailing list Free

Re: [Freesurfer] Help with V6

Hello Noah, Could you be more specific as to how you were able to resolve this problem? What additional tweaks were necessary? I too received the same error message: ERROR: Flag -subfields-T1 unrecognized. -all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1 Darwin glenn-stebbins-computer.local 12

[Freesurfer] -3T & -wsthresh Flags

Hello FreeSurfer exports, I have two questions regarding recon-all flags: 1) Our data was obtained with a 3T scanner. Would you recommend that all 3T data be run thorough the recon-all stream with the -3T flag? 2) One subject has part of the left occipital lobe cut during the skullstripping pr

Re: [Freesurfer] Hyperintense WM & WM Deletions

the same problem using the same coil (GE 750; mainly occipital pole), so any suggestions for how to correct this would be very helpful. Thanks! Anthony On 1/5/15, 7:05 PM, Douglas Merkitch wrote: Hello Freesurfer experts, We have T1 data from a 3T GE 32-channel head coil that exhibits areas

[Freesurfer] Hyperintense WM & WM Deletions

Hello Freesurfer experts, We have T1 data from a 3T GE 32-channel head coil that exhibits areas of hyperintense white matter. Specifically there are areas of the wm.mgz on the periphery with values ranging from 117-121, which lead to overextending/overestimation of the wm.mgz. 1) Can anyone su

Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

nitialization and then fine tunes them. So you also have to check the surfaces in the base are all OK. That is essential as long takes it from there. Best, Martin On 05/16/2014 12:29 PM, Douglas Merkitch wrote: Dear Martin and FreeSurfer experts, Thanks for your response. I have just finished re

Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

d it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz

[Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved

[Freesurfer] aseg stats left/right-vessel

Hello all, What exactly is included in the Left/Right Vessel labels? I've found hints as to what they are, but no exact definition. Thanks in advance! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu