[Freesurfer] autmatic image with panel of hemisphere made by script

I have used Tksurfer to make image from cross subject statistics maps in mgh files. Is it possible to use a script to make image with both hemisphere in lateral and medial view. I would also like to display p values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How can I produce im

Re: [Freesurfer] autmatic image with panel of hemisphere made by script

Hi Knut you can use a tcl script in tksurfer if you want. You are probably better off doing the 10^-log(p) on your own and saving it as a separate overlay. There are plenty of tcl scripts in the distribution as examples. A simple one would be: set val $home/$subject/label/$hemi.your_overlay.m

Re: [Freesurfer] Conversion of an mgh file to nii (fwd)

FYI -- Forwarded message -- Date: Tue, 7 Feb 2012 09:15:37 -0500 From: Ziad Saad To: Bruce Fischl Subject: Re: [Freesurfer] Conversion of an mgh file to nii I just realized my post got rejected from the message list since I I am not a subscriber. Could you throw it up there fo

Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

Hi - It's hard to tell without access to the actual data, but it sounds like you've found the right way to reconcile your nifti volume and gradient directions, so you should pass those to trac-all directly instead of the dicom. Anastasia. On Tue, 7 Feb 2012, Xiangzhen Kong wrote: Hi Yen

[Freesurfer] mris_divide_parcellation

Dear Freesurfer experts, I have a question regarding mris_divide_parcellation. I have created a file containing the parcels from aparc.annot that I want to split and I have run the following command. Why is Freesurfer allocating 36 additional units? When I open the new annotation file (rh.aparc.sp

Re: [Freesurfer] mris_divide_parcellation

Hi Yolanda does the resulting parcellation look ok? I think that's a small bug that may not have any effect on you (there will just be extra, unused color table entries) Bruce On Tue, 7 Feb 2012, Yolanda Vives wrote: Dear Freesurfer experts, I have a question regarding mris_divide_parcella

[Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh

Hi Experts, Is there a way to add the CA-4/DG subfield to the output generated by kvlQuantifyHippocampalSubfieldSegmentations.sh? Running the command for an individual subject outputs this subfield, but I wanted to make sure there wasn't an easier route before I start manually entering each subje

[Freesurfer] A question about testing the installation

Hi all, I have a question about FS installation. Finally I installed FS, but not sure it is complete. For testing FS installation, when I wrote tkmedit bert orig.mgz, It says: Couldn't create output file .xdebug_tkmeditReading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/f

[Freesurfer] Registration for Upcoming Freesurfer Course, April 2-4

The Freesurfer group will be offering a three-day Freesurfer Tutorial and Workshop, April 2-4 at the Martinos Center in Charlestown, MA. A description of the course, the tentative schedule, and the link to the registration website can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/Cours

Re: [Freesurfer] Hippo-subfield fault

Hi Rob, It seems the internal 5.1 version of FreeSurfer you're running was somehow compiled on 12 April 2011 (?), whereas the official release date was 24 May 2011. Could you please double-check if this is indeed the case? If it is, could you please run the official release instead? We changed a

Re: [Freesurfer] Hippocampal subfield: average standard T1 ore use higher resolution

Hi Oliver, You're right: internally we're upsampling the images to 0.5mm isotropic resolution, so if you had acquired 0.5mm isotropic images from the start, that would actually be much better (provided you don't simply trade off SNR for increased image matrix size). The catch with this is that the

Re: [Freesurfer] Problem viewing hippo-subfields

Hi Rob, I think this might be related to the same 5.1 version mismatch I indicated in my previous email to you. Could you please try if things start working when you use the official FS release? Thanks, Koen On Mon, Feb 6, 2012 at 1:59 PM, Rob Tennyson wrote: > Hi Experts, > > So I found a s

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh

Hi Rob, Same reply - the current scripts should do this automatically for you... Please let me know if you run into trouble with this, Koen On Tue, Feb 7, 2012 at 11:18 AM, Rob Tennyson wrote: > Hi Experts, > > Is there a way to add the CA-4/DG subfield to the output generated > by kvlQuantif

Re: [Freesurfer] autmatic image with panel of hemisphere made by script

you could create each of the individual maps, but not the placement and not the tet On Tue, 7 Feb 2012, Knut J Bjuland wrote: > Hi Bruce > > > Is it possible to use ascript to create a similar figure to the jpg file I am > attaching? > > Knut J > > > > On 07. feb. 2012 15:09, Bruce Fischl wrote:

Re: [Freesurfer] autmatic image with panel of hemisphere made by script

Hi Knut, you can check out my script called tksnap (uses accopanying mytks.tcl). It will take pics in different orientations. Note: this is not a supported script, so it's up to you to figure out what it does and how it does it. I provide it as a way to help you figure this stuff out. If you do

[Freesurfer] Large part of brain missing from wm.mgz and surfs

Hi all, My lab is just starting to use Freesurfer, and are finding that a lot of our recon-all jobs are needing a fair amount of editing. We've run into a problem that we can't figure out how to address - on several of our brains, a large chunk (up to 2/3 of the brain) is missing from the wm.mgz f

Re: [Freesurfer] Large part of brain missing from wm.mgz and surfs

Hi Nicole do you want to upload an example subject directory tarred and gzipped? We almost never see this, so it sounds like something is wrong. cheers Bruce On Tue, 7 Feb 2012, Nicole Senecal wrote: > Hi all, > My lab is just starting to use Freesurfer, and are finding that a lot of our > re

[Freesurfer] Repost: question regarding my contrast

Dear FreeSurfers, I have been doing some basic cortical thickness analyses, which all went good. Now I want to analyze some additional things, and I want to make sure that my contrast files are ok. Could you help me out or give me advice? So, I have three groups (control - MCI - Alzheimer) and

Re: [Freesurfer] Repost: question regarding my contrast

Hi Heidi, the first contrast is correct assuming that BP is your 2nd variable. For the second design, you would make use [0 0 1 -1 0 0]. Note that you can do all of these from a single FSGD file (but using separate ones is ok too). doug Jacobs H (NP) wrote: > Dear FreeSurfers, > > I have been

[Freesurfer] Question about ?h.sulc and ?h.curv

Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change,

[Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years

Re: [Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Hi Mark, So the first thing is you absolutely need to re-run you 1st year data with 5.1 The reason is that you will introduce potential bias by running the different time points with different software (consistently). As a side note: The same is basically true when they do software updates on the

Re: [Freesurfer] autmatic image with panel of hemisphere made by script

Hi, On the off chance that you are comfortable with Python, you may find that PySurfer provides a more pleasant scripting environment than the tcl-based TkSurfer interface :) Best, Michael On Tue, Feb 7, 2012 at 12:46 PM, Douglas N Greve wrote: > Hi Knut, you can c