Re: [Freesurfer] Making Anatomical Mass for optical data
Hi Mark why go to a standard space? It's probably easier to stay in the subject coordinate system. The aparc+aseg.mgz contains all the cortical and subcortical labels you want, defined in $FREESURFER_HOME/FreeSurferColotLUT.txt. You can extract individual labels to create binary masks either using mri_binarize --match or mri_extract_label. You'll need to map them into functional coordinates with mri_vol2vol after creating a registration between them (usually with bbregister). cheers Bruce On Wed, 8 Aug 2012, Mark Fletcher wrote: Dear FreeSurfer Developers, Currently we are trying to analyze our functional data (optical imaging) using ROI?s that are defined on the basis of FreeSurfer Segmentation. In order to do this, we need a 3 dimensional mask in which a particular region as identified by FreeSurfer is used as a mask for analyzing our functional data. How can we output from FreeSurfer what each voxel is classified as (hippocampus, etc.), or a mask having a value of 1 for each region, and a 0 for every other voxel. Also, what coordinate space would this be in? We would prefer either MNI or TAI (or a way to get into either space). Thanks you so much for your help. Sincerely, Mark Fletcher CNL Lab UIUC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] asking about seed/target ROIs in TRACULA
Hi Juke - The end ROIs are obtained by dilating the end points of the training streamlines from the tract atlas and finding their intersection with the cortex of the test subject. Hope this helps, a.y On Thu, 9 Aug 2012, Juke Cha wrote: Hi, I'm wondering if I can get any information about ROIs being used in the global tractography procedure in TRACULA. I'm particularly interested in the uncinate fasciculus. I've searched for such information in the website and the article, to no avail. Thanks for your help! Best, Juke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf or mri_cor2label
Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_vol2surf or mri_cor2label
Hi, you should use mri_cor2label. Bests, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: ta...@mpibpc.mpg.de -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Stephanie Rossi Sent: Thursday, August 09, 2012 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_vol2surf or mri_cor2label Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ico4 parcellation and mri_segstats
Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something? Thanks, -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_vol2surf or mri_cor2label
The syntax is a bit different from what you can fin din the wiki: mri_cor2label --i label.nii.gz --l label.label --id 1 will convert label.nii.gz to label.label containing 1 for each voxel. Cheers, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: ta...@mpibpc.mpg.de -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Stephanie Rossi Sent: Thursday, August 09, 2012 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_vol2surf or mri_cor2label Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf or mri_cor2label
Hi again, We've done the conversion, but the position of the label is not correct. We derived our masks from fsl HarvardOxford atlas and then obtained individual subjects masks. Should we apply any registration matrix for the freesurfer environment before we run mri_cor2label? Thank you, Stephanie The syntax is a bit different from what you can fin din the wiki: mri_cor2label --i label.nii.gz --l label.label --id 1 will convert label.nii.gz to label.label containing 1 for each voxel. Cheers, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: ta...@mpibpc.mpg.de -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Stephanie Rossi Sent: Thursday, August 09, 2012 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_vol2surf or mri_cor2label Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
HI I am unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol. Could you pleas add the file back. Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
ok, try now On 08/09/2012 02:28 PM, Knut J Bjuland wrote: HI I am unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol. Could you pleas add the file back. Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert downsample then resample shifts image upward one voxel
I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and then again back up to 1mm isotropic space. The resultant image shifted up a voxel from the original converted straght to nii.gz. This points to the resampling procedure, and not the conversion to different file format. Suggestions? Note: I wanted to hand trace the hippocampus in the norm.mgz, and upsampled the norm.mgz to trace on. I traced it, and then downsampled to 1mm to compare with Freesurfer segmentation, but found it shifted. Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
