Hi Bruce,
Thanks for the quick response. Sorry, I meant 6mm radius (for regions such as fusiform face area and visual word form area). I am using the same seeds that are suggested to be associated with reading in the following study. I am wondering whether any guidelines have been set for determining seed size on surface from comparable volume based studies when that seed is a sphere or cube of voxels. I will be doing something similar using the peak coordinates of the components DMN suggested by Yeo 2011.
Koyama, M. S., Kelly, C., Shehzad, Z., Penesetti, D., Castellanos, F. X., & Milham, M. P. (2010). Reading Networks at Rest. Cerebral Cortex, 20(11), 2549–2559. http://doi.org/10.1093/cercor/bhq005
Many thanks Erik Jahner
Sent from my iPad
On Apr 5, 2017, at 7:12 AM, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: Can anyone help with this error - trying to compare 2 scans in same person (Martin Reuter)
- Generate stat file of ROI voxel sizes (Ostrowski, Lauren)
- Reminder: 3.5-year Postdoc Position in Social Neuroscience at Bangor University, UK (Kami Koldewyn)
- Re: Custom color maps (dg wakeman)
- Re: ROI seed size (Bruce Fischl)
- PROGRAM DIRECTOR POSITION IN COGNITIVE NEUROSCIENCE AT NSF: Application deadline May 11, 2017 (Uri Hasson)
- Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams (David Semanek)
- Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams (Octavian Lie)
- Re: Comparing LME models (Bronwyn Overs)
- Re: Registration of both the brain and the "surf" files to the same template. (Douglas Greve)
- Re: Volume to Surface mapping looks great for Vols created in FSL but not SPM (Douglas Greve)
- Re: Volume to Surface mapping looks great for Vols created in FSL but not SPM (Rita Elena Loiotile)
- Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams (Martin Reuter)
- Surface Integral Questions (Levman, Jacob)
- Re: Volume to Surface mapping looks great for Vols created in FSL but not SPM (Douglas Greve)
- Re: Qdec effect sizes, correlation coefficient (Douglas Greve)
- Changing the Orientation of Scan Slices (Images included) (Jeffrey Crawford)
Message: 1 Date: Tue, 4 Apr 2017 18:17:16 +0200 From: Martin Reuter mreuter@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Can anyone help with this error - trying to compare 2 scans in same person To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1dec67aa-6ef5-1ea2-4241-b578b5213173@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
Hi Brad,
the base commands needs a space before -tp
recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all
check if the directory 005_IHD_1_base exists. Also check if this file exits: /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm
Best, Martin
On 04/04/2017 05:55 PM, Brad Matushewski wrote:
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Brad Matushewski *Sent:* March 30, 2017 2:38 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Trying to compare 2 scans from same person, 6 months apart.
First scan is 005_IHD_1
Second scan is 005_IHD_1_post
These were in $SUBJECTS / ihd
I moved them into $SUBJECTS
(i.e. no subfolder within $SUBJECTS folder).
I am following this;
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing
FsTutorial/LongProcessing - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing
surfer.nmr.mgh.harvard.edu
Processing your data consists of three steps: First, run all your data independently (we also say cross sectionally) using "recon-all -all" (i.e. all time points for ...
I ran a normal recon all on both scans first.
I then ran this command:
recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all
and all seemed well.
I then tried to run this command.
recon-all -long <tpNid> <templateID> -all
This is how I entered the command:
recon-all -long 005_IHD_1 005_IHD_1_base -all
It resulted in errors...here is the last bit of the error log:
Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 30 14:31:07 EDT 2017 /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri
cp /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm
cp: cannot stat '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': No such file or directory Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu Mar 30 14:31:07 EDT 2017
What went wrong?
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