[Freesurfer] -addtp option not working in recon-all -long

Hi all, I wanted to add a new timepoint in my longitudinal stream without recreating the base template. recon-all -help shows that I should be able to do that with: recon-all -long -addtp -all However, when I tried it I get an error. Here is the error: $recon-all -long miriad_189_AD_M_10Simula

[Freesurfer] What exactly was wrong with DOSS in QDEC

Hello, I am dealing again with the "old" issue of using DOSS in QDEC. This option was removed. I cannot find any detailed explanations of what exactly was wrongly computed when selecting DOSS. I only find as explanation: "that there may be a bug in the way that QDEC computes contrasts for DOSS"

Re: [Freesurfer] Desikan-Kilany atlas

​Thanks for your reply Bruce, however I get an error when try to use this command. I'm in the directory containing the files and I ran *mri_surf2vol --surfval lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs --hemi lh --outvol LH.nii* and it gave me an output of *ERROR: cannot recog

Re: [Freesurfer] Desikan-Kilany atlas

Hi Norman don't give it the gcs file as input - that's the atlas. Give it the lh.aparc.annot for that subject cheers Bruce On Wed, 25 Feb 2015, Norman Benbrahim wrote: ​Thanks for your reply Bruce, however I get an error when try to use this command. I'm in the directory containing the fil

[Freesurfer] Analyze format

Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the

Re: [Freesurfer] Analyze format

Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruc

[Freesurfer] A->P to P->A on GE 3T Discovery MR750

Hi Everyone, In order to introduce distortion correction methods in our DTI processing pipeline, I wanted to acquire B=0 with A->P to P->A phase encode directions, as recommended by topup tutorials. I talked to the MRI operators at our facility, and they were not able to find out how to fli

Re: [Freesurfer] long_mris_slopes error

Hi Carolina, probably you are not interested in the average thickness, so you can drop --do-avg . Also usually people decide between pc1 and spc. The stack is also not really necessary unless you want to look at it. Try to remove the trailing / at fsaverage and --sd $SUBJECTS_DIR that should

Re: [Freesurfer] -addtp option not working in recon-all -long

Hi Bishesh, that is weird, it should add the time point to that file. What version of FS are you using? Best, Martin On 02/25/2015 06:03 AM, Bishesh Khanal wrote: Hi all, I wanted to add a new timepoint in my longitudinal stream without recreating the base template. recon-all -help shows th

[Freesurfer] Any short route to parcellate only?

Hi folks, I am using the parcellation of Freesurfer for some other analyses. I see that the parcellation if obtained rather late in the pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all However, asking does not hurt: is there any short route to get the Desikan parcellation without doin

Re: [Freesurfer] Any short route to parcellate only?

Hi Dorian, no, sorry, you pretty much need to run everything to get it. cheers Bruce On Wed, 25 Feb 2015, Dorian P. wrote: Hi folks, I am using the parcellation of Freesurfer for some other analyses. I see that the parcellation if obtained rather late in the pipeline: http://surfer.nmr.mgh.h

[Freesurfer] trac all -p

Hi Anastasia: I have run trac-all using the following command: trac-all -prep -c /data/alanf/FreeSurfer_5.3/diffusion_recons/dmrirc-101309 However, I get an error message which is as follows: INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons INFO: Diffusion root is /data/alanf

[Freesurfer] Convert between .m3z and .tm3d format outputs from mri_cvs_register

I using mri_cvs_register and applyMorph on a linux server ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I would like to be able to convert the output transform *.m3z to *.tm3d format, as using applyMorph with the .m3z file returns an error: After loading template extension = m3z te

Re: [Freesurfer] trac all -p

Hi Alan - It can't find the file. Check the error message, part of the path to the file is repeated twice. I suspect you typed that part in both dcmroot and dcmlist. a.y On Wed, 25 Feb 2015, Alan Francis wrote: Hi Anastasia: I have run trac-all  using the following command: trac-all -prep

Re: [Freesurfer] Convert between .m3z and .tm3d format outputs from mri_cvs_register

You can use createMorph: createMorph --out $tm3d --template $template \ --subject $moving --in gcam $m3z --Lilla On Wed, 25 Feb 2015, Zachary Greenberg wrote: I using mri_cvs_register and applyMorph on a linux server ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I wo

Re: [Freesurfer] -addtp option not working in recon-all -long

It's 5.3.0. Here is the freesurfer version and my system info: Build stamp: freesurfer-Linux-centos6_x86_ 64-stable-pub-v5.3.0 RedHat release: Fedora release 19 (Schrödinger’s Cat) Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64 On Wed, Feb 25, 2015 at 7:54 PM, Martin Reuter wrote: > Hi B

[Freesurfer] [FreeSurfer/TRACULA]

Hello, Where can we find the link to tract the inferior fronto-occipital fascicles? Just want to know the reference name to add it to my path list. Best, Walid ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] warping segmentations onto unprocessed brain

Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I

Re: [Freesurfer] warping segmentations onto unprocessed brain

Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce > On Feb 25, 2015, at 11:18 PM, David Grayson wrote: > > Hi freesurfers, > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to

Re: [Freesurfer] [FreeSurfer/TRACULA]

This tract is not included in our atlas. Please see the wiki for a list of available tracts. On Thu, 26 Feb 2015, Walid Yassin wrote: Hello, Where can we find the link to tract the inferior fronto-occipital fascicles? Just want to know the reference name to add it to my path list. Best,

Re: [Freesurfer] warping segmentations onto unprocessed brain

Hey Bruce, Thanks for responding. I would actually prefer nonlinear. I did not mention it, but the aseg data that I have is on a distortion-corrected T1 image, whereas the unprocessed image I want to warp onto is the same scan but not corrected for distortion. The distortions are nonlinear. I was