[Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI

Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id:

[Freesurfer] brain orientation in qdec

Dear experts, I ran recon-all with qcache. When loading the right hemisphere of fsaverage (or any other surface reconstruction) into tksurfer (for example command: tksurfer fsaverage rh white), the left hemisphere surface is displayed, and it is upside down. When I import annotations they

Re: [Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI

Hi Muhammad try: set sdir=/home/naveed/freesurfer/subjects/CHR01/surf mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik cheers Bruce On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI

[Freesurfer] recon-all error

Hello Happy New Year! I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached. All the best throughout 2014! Emad Emad Ahmadi, MD

Re: [Freesurfer] Fwd: Anatomical segmentation - question

it probably doesn't matter, but Doug is the Talairach expert, so perhaps he can comment Bruce On Mon, 6 Jan 2014, Rotem Saar wrote: Dear freesurfer experts, I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing

[Freesurfer] MNC label to Freesurfer

Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number,

Re: [Freesurfer] MNC label to Freesurfer

Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up

[Freesurfer] Are two T1 scans helpful for better recon-all?

Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list

Re: [Freesurfer] MNC label to Freesurfer

Than you can use mri_binarize with the --match flag. --match matchval --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert

Re: [Freesurfer] Are two T1 scans helpful for better recon-all?

Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an

Re: [Freesurfer] Are two T1 scans helpful for better recon-all?

Thank you so much, Bruce. On Mon, Jan 6, 2014 at 3:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due

Re: [Freesurfer] MNC label to Freesurfer

Hi Caspar can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject? cheers Bruce On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Lilla, unfortunately, there is no correspondence

Re: [Freesurfer] FW: recon-all exited w/errors

oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the

Re: [Freesurfer] MNC label to Freesurfer

Hi Bruce and Lilla, I have a MNC volume that contains area labels, ie voxels belonging to one label all have the same intensity value. I am trying to get this converted into Freesurfer label files for further analysis in volume space. Following Lilla's advice, I am first using mri_binarize with

[Freesurfer] FW: FW: recon-all exited w/errors

Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric,

Re: [Freesurfer] FW: FW: recon-all exited w/errors

what is the slice thickness? Usually we recommend no dimension be thicker than 1.5mm or so On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica

Re: [Freesurfer] FW: FW: recon-all exited w/errors

Its 1mm! But I found a newer study for the subject, so I will try this new one and if it still does not work, I will email back! Thanks so much again! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 4:27 PM To: Boric,

Re: [Freesurfer] FW: FW: recon-all exited w/errors

1mm and 60 slices covers the whole brain? Usually it requires more like 160 slices. On Mon, 6 Jan 2014, Boric, Katica A. wrote: Its 1mm! But I found a newer study for the subject, so I will try this new one and if it still does not work, I will email back! Thanks so much again! Katica

[Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon

Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly

Re: [Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon

Not sure. Try running mri_convert 001.dcm deleteme.mgh if it fails, capture the screen output and send it to the list doug On 01/06/2014 06:31 PM, Anders Olsen wrote: Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with