Re: [Freesurfer] spatialsmooth-sess with option to set mask file name

Hi Doug, I found a way to build it in myself. I am using spatialsmooth-sess from v5.1. I need to smooth some functional data that I have preprocessed through some other program until this point. What should I be using instead of spatialsmooth-sess if I only want to smooth? Thanks, Caspar On Thursd

Re: [Freesurfer] spatialsmooth-sess with option to set mask file name

No, sorry. Why are you using such an old version? doug On 1/9/14 5:26 PM, Caspar M. Schwiedrzik wrote: Hi Doug, do you have a version of spatialsmooth-sess with the option to set mask file name? Thanks, Caspar ___ Freesurfer mailing list Free

[Freesurfer] problem with bvecs file with new (12/13) TRACULA code

Hi, I am re-running GE acquired 3T product DTI data which ran without trouble through the older tracula code. However, now when I run the code, the bvec file that gets generated has an extra 0 placed at the very end, and then trac-all -prep eventually fails because it complains the bvec and bvals

Re: [Freesurfer] questions about cortical thickness using qdec.

On 01/09/2014 05:15 PM, yaya ya wrote: > > > > On Thu, Jan 9, 2014 at 10:56 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > On 01/09/2014 04:42 PM, yaya ya wrote: > > I am sorry for this misunderstanding. > > > > I am now performing surface-based analysis on

[Freesurfer] spatialsmooth-sess with option to set mask file name

Hi Doug, do you have a version of spatialsmooth-sess with the option to set mask file name? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-

Re: [Freesurfer] Download FS not working?

Please be absolutely sure you are trying from other networks because I just tested it and it worked. We frequently get emails like this and in every case I can remember it was always solved by using another network. Freeesurfer is a large file 3.5Gb and many networks place limits on files that

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Hi Doug, many thanks for your help! This is the command i used: mri_label2vol --label lh.parstriangularis.label --temp $DIR/mri/orig.mgz --subject sub${isub} --hemi lh --o $OUTDIR/labels/sub${isub}_parstriangularis.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg $OUTDIR/labels/sub${isub}_regist

Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

Pablo, I do not see the attachment. It may have been filtered because the freesurfer list has fairly strict file attachment size restrictions. Feel free to send me the recon-all.log directly at zkauf...@nmr.mgh.harvard.edu However, depending on the processor, I am not surprised your ~10hr run

Re: [Freesurfer] questions about cortical thickness using qdec.

On 01/09/2014 04:42 PM, yaya ya wrote: > I am sorry for this misunderstanding. > > I am now performing surface-based analysis on my data, especially on > cortical thickness. Since when I did this analysis based on the whole > left or right hemisphere, the results were not very good. > > That is

Re: [Freesurfer] questions about cortical thickness using qdec.

I'm still not sure I understand what you are doing. Is it a volume-based analysis or a surface-based analysis? You would only use a brain mask or a surface mask for a volume-based analysis. doug On 01/09/2014 04:15 PM, yaya ya wrote: > Thank you very much for your patience, douglas. > > I just

Re: [Freesurfer] questions about cortical thickness using qdec.

Thank you very much for your patience, douglas. I just want to create a surface mask. What you said is use mri_annotation2label to create a surface mask. Then when do mri_glmfit analysis on the surface, I need to use the flag --label my surface mask. If my understanding is wrong, don't hesitate t

Re: [Freesurfer] questions about cortical thickness using qdec.

Is this an analysis of volume/voxel data or surface/vertex data? If surface, then you'll need to extract the left insula label from lh.aparc.annot (use mri_annotation2label), then pass this label to mri_glmfit with --label doug On 01/09/2014 03:52 PM, yaya ya wrote: > Thanks, Doug. > > I jus

Re: [Freesurfer] questions about cortical thickness using qdec.

Thanks, Doug. I just searched the list to find how to generate a mask. Let us say the surface of the left insula. It seems that I need to use mri_mask command and the brain which I use to get the mask should be brainmask.mgz in the fsaverage, right? Then I use this mask in mri_glmfit command. A

[Freesurfer] Download FS not working?

Hi guys, I've been trying in the last days to download FS but it doesn't seem to work: winkler@volans:~ $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz --2014-01-09 20:47:12-- ftp://surfer.nmr.mgh.har

Re: [Freesurfer] questions about cortical thickness using qdec.

On 01/09/2014 02:18 PM, yaya ya wrote: > Dear Doug, > > I am sorry. It is my first time to post the message in this way. I am > now used to it:) > > The results from the contrast 0 0 1 -1 did not survive the multiple > comparision corrections. In other words, I guess that it should imply > that

Re: [Freesurfer] questions about cortical thickness using qdec.

Dear Doug, I am sorry. It is my first time to post the message in this way. I am now used to it:) The results from the contrast 0 0 1 -1 did not survive the multiple comparision corrections. In other words, I guess that it should imply that I could try DOSS. If my thought is wrong, please feel f

[Freesurfer] QAtools_v1.1 package

Hi Vinke, In the QAtools_v1.1 package, should the supplied DefaultAsegMeans.txt file have "0 +/- 0" as all its entries? More generally, I was wondering what aspects of the QAtools package you've found most useful?  In particular, do the results from wm-anat-snr relate to data quality in a me

Re: [Freesurfer] xhemi correct for multiple comparisons

great thanks Doug! Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices. Thanks, Krista On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve wrote: > > Yes,

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

Thanks Doug! just editing to correct a minor error in the last question: > 3.- Afterwards I want to run probtracx with the following command (my > doubt is mainly about the files to use, since FSL files are RAS, > freesurfer anatomicals are LIA and freesurfer diffusion are LAS, are > all the files

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

On 01/09/2014 12:45 PM, Garikoitz Lerma-Usabiaga wrote: > Hi Anastasia, > I want to use a hippocampal subfield as a seed in FSL. I am having > problems understanding how to change spaces around... > > 1.- Is this command ok? > mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ > mri/hippo_subfield_i

[Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

Hi Anastasia, I want to use a hippocampal subfield as a seed in FSL. I am having problems understanding how to change spaces around... 1.- Is this command ok? mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o mri/hippo_subfield_in_

Re: [Freesurfer] Question about qdec analysis

On 01/09/2014 08:00 AM, car...@van-vlodrop.de wrote: > > Dear freesurfer community, > > I'm trying to do my analysis in qdec right now with the question of > differences of cortical-thickness between patient and control. > > Instead I have a few questions about the different modulations in qdec:

Re: [Freesurfer] xhemi vertices

Hi Sofie, please remember to post to the list. The trickiness is that if you map the lh to the rh, then there will be interpoolation in the lh that is not in the rh which can cause a false difference. Our symmetric stream is set up to avoid this problem. doug On 01/09/2014 04:39 AM, Sofie V

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Frank, can you send the commands you used and the terminal output? doug On 01/09/2014 04:35 AM, Frank Hsieh wrote: > Hi Gari, Thanks so much for the tips! > @ Doug: I basically followed the instructions on this site >

Re: [Freesurfer] questions about cortical thickness using qdec.

Please remember to post to the list. For the 0 0 1 -1 contrast, did any results survive multiple comparisons correction? If so, then at least the voxels in that region cannot be used with DOSS. I'm not sure why the patter was opposite between the two contrasts. I could mean that there is a non

Re: [Freesurfer] Question about Monte Carlo and significant clusters

Is this in QDEC? Are you clicking on the correct item in the list. I think that there should be labels for each signfificant cluster doug On 01/09/2014 01:47 AM, Maller, Jerome wrote: > > Hi everyone, > > I have a question related to Monte Carlo tests of multiple > comparisons. When I conduct s

Re: [Freesurfer] Fwd: Anatomical segmentation - question

Hi Rotem, can you repost the question? The email got reformatted and is impossible to read. thanks doug On 01/09/2014 01:16 AM, Rotem Saar wrote: > Hi Doug, > > Can u help ? > > Thanks > Rotem > > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Ne

Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

Dear Zeke,I am forwarding the email below that I believe it got lost in the dense list of correspondences.I would highly appreciate your input.Thanks,Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 19 Dec 2013 15:27:11 + Subject: Re: [Freesurfer] Output of reco

Re: [Freesurfer] Freesurfer templates for cross-ethnicity comparisons

Hi Mike nice to be right once in a while :). You shouldn't have to register to an atlas brain to build the folding pattern template though - you can pick one of your own dataset to start with. cheers Bruce On Thu, 9 Jan 2014, Michael Chee wrote: Hi Bruce and Linda, Yes, this is my work e

[Freesurfer] Question about qdec analysis

Dear freesurfer community, I'm trying to do my analysis in qdec right now with the question of differences of cortical-thickness between patient and control. Instead I have a few questions about the different modulations in qdec: In 'Design' it's possible to choose from different measurements.

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this siteto obtain my ROIs. Any thoughts? Many thanks! Frank On Thu, Jan 9, 2014 at 1:22 AM, Gari

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is: 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select i

[Freesurfer] Fwd: questions about cortical thickness using qdec.

Dear Greve, Thank you very much for your response. I am now a little more clear, although I still have some further questions. According to your suggestion, I just tried to test whether there is a difference between group age. I included age as a continuous variable in qdec. After running, I got