Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space
Hi Doug, Thanks very much!! Best, Daniel On Jul 16, 2013, at 9:14 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz. However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space? Many thanks!! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] bvecs error from Tracula
Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ 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] Missing flirt.fsl file in bin folder
Hello freesurfers, I’ve been trying to run tracula on freesurfer and it seems that when I get to the point where it uses FSL’s flirt I receive an error. I looked into it further and it seems I am missing a file to run flirt: $FREESURFER_HOME/bin/flirt.fsl It seems that I somehow do not have that file to complete tracula. I was hoping someone could help with this or perhaps send me the file? I am using freesurfer- Darwin-snowleopard-i686-stable-pub-v5.3.0- MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Hope to hear from someone soon, Andrew ___ 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] Propagating changes to segmentation
Hello, I have a question about propagating changes to segmentation. Once I have saved my edits what is the appropriate command to propagate these changes for both cortical and subcortical changes that I have made. The workflow instructs that after segmentation edits are made to run -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3 to the wm. mgz file. However the instructions indicate to open brainmask.mgz to make edits. Should I make changes on the wm.mgz file? Any clarification on this topic would be much appreciated. -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine ___ 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] Freesurfer installation
Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup But after the installations when I open the terminal nothing happens. I also tried to launch freesurfer this way: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If I do this I get: command not found command not found command not found Any advice on how to finally set up the software would be great help. Thank you in anticipation.Pablo ___ 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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ 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] Freesurfer installation
Pablo, That page describes how to setup a personal laptop for usage in the Freesurfer course. It does not apply to a standard freesurfer installation. Try opening a new terminal and typing bash before the export and source commands you give below. -Zeke On 07/17/2013 10:27 AM, pablo najt wrote: Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup But after the installations when I open the terminal nothing happens. I also tried to launch freesurfer this way: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If I do this I get: command not found command not found command not found Any advice on how to finally set up the software would be great help. Thank you in anticipation. Pablo ___ 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 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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] bvecs error from Tracula
Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ 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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
Hi Eugenio, We are using version 5.1. I attached our script. We added to line 60, setting the subject directory. We also changed the statFileName (see line 291 on the attached script). I should also note that the volumeStats_left and right text files within each subject's mri folder is empty. Thanks for your help. On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu wrote: Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. kvlQuantifyHippocampalSubfieldSegmentations.sh Description: Bourne shell script ___ 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] SWI acquisition question
Hi Panos sorry, I think this is pretty far outside our expertise, and it would be hard in any case to try to figure out what happened to give you these strange looking results. I certainly don't have any insight sorry, Bruce On Wed, 17 Jul 2013, Fotiadis, Panagiotis wrote: Hi FS Community, I was wondering whether anyone had a chance to look into this. Thanks again for your time! Best, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, July 16, 2013 2:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SWI acquisition question Hi FreeSurfer community, I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, 2) Is it normal for the mIP to look like that? Usually it looks different, and 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. Thank you in advance for your help and time! Best, Panos ___ 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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
OK, then the question is why kvlQuantifyPosteriorProbabilityImages is producing an empty file I think the problem is that kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different way depending on the number arguments, etc. I would suggest that you go back to the original version of the script, and use it the way it's described in http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation, that is, setting the environment variable SUBJECTS_DIR and calling the script without arguments. Kind regards, /Eugenio On 07/17/2013 11:46 AM, Jasmeet Hayes wrote: Hi Eugenio, We are using version 5.1. I attached our script. We added to line 60, setting the subject directory. We also changed the statFileName (see line 291 on the attached script). I should also note that the volumeStats_left and right text files within each subject's mri folder is empty. Thanks for your help. On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] convert DK atlas ROI to .nii.gz in MNI space
Hi Doug, Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for --temp? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual? Great thanks! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 7/16/13 9:13 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz. However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space? Many thanks!! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://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 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] convert DK atlas ROI to .nii.gz in MNI space
does htis answer your question? It is from running mri_label2vol with --help doug --temp tempvolid Template volume. The output volume will have the same size and geometry as the template. Template must have geometry information (ie, direction cosines and voxel sizes). Required. On 07/17/2013 12:11 PM, Yang, Daniel wrote: Hi Doug, Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for --temp? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual? Great thanks! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 7/16/13 9:13 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz. However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space? Many thanks!! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Missing flirt.fsl file in bin folder
Hello, Individuals who downloaded Freesurfer v5.3 for snow leopard (32bit) will be missing six fsl routines. A patch has been created and can be downloaded from this link: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer_fsl.tar.gz To apply the patch, simply extract the contents of the above file into the /Applications/freesurfer/bin directory. This should result in six new files in the /Applications/freesurfer/bin directory all with the .fsl extension. -Zeke On 07/17/2013 09:33 AM, Gundran, Andrew wrote: Hello freesurfers, I’ve been trying to run tracula on freesurfer and it seems that when I get to the point where it uses FSL’s flirt I receive an error. I looked into it further and it seems I am missing a file to run flirt: $FREESURFER_HOME/bin/flirt.fsl It seems that I somehow do not have that file to complete tracula. I was hoping someone could help with this or perhaps send me the file? I am using freesurfer- Darwin-snowleopard-i686-stable-pub-v5.3.0- MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Hope to hear from someone soon, Andrew ___ 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 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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
That worked, thanks for your help! On Wed, Jul 17, 2013 at 12:00 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu wrote: OK, then the question is why kvlQuantifyPosteriorProbabilityImages is producing an empty file I think the problem is that kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different way depending on the number arguments, etc. I would suggest that you go back to the original version of the script, and use it the way it's described in http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation, that is, setting the environment variable SUBJECTS_DIR and calling the script without arguments. Kind regards, /Eugenio On 07/17/2013 11:46 AM, Jasmeet Hayes wrote: Hi Eugenio, We are using version 5.1. I attached our script. We added to line 60, setting the subject directory. We also changed the statFileName (see line 291 on the attached script). I should also note that the volumeStats_left and right text files within each subject's mri folder is empty. Thanks for your help. On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu wrote: Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] SWI acquisition question
Hi Bruce, Don't worry about it! In addition, I was wondering about something else as well. I've been using MRIcron to analyze some of my Susceptibility Clinical Scans and even though they used to open fine, some of them (like the one I have attached in this email) appear distorted in a way. In the images I attached the Original one is how the Susceptibility clinical image should appear like, and the Distorted is how it appears for some of my subjects. Would you happen to know why is this happening? Thanks again for your time and help! Best, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 17, 2013 11:54 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SWI acquisition question Hi Panos sorry, I think this is pretty far outside our expertise, and it would be hard in any case to try to figure out what happened to give you these strange looking results. I certainly don't have any insight sorry, Bruce On Wed, 17 Jul 2013, Fotiadis, Panagiotis wrote: Hi FS Community, I was wondering whether anyone had a chance to look into this. Thanks again for your time! Best, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, July 16, 2013 2:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SWI acquisition question Hi FreeSurfer community, I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, 2) Is it normal for the mIP to look like that? Usually it looks different, and 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. Thank you in advance for your help and time! Best, Panos attachment: Distorted.jpegattachment: Original.jpeg___ 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] Gray matter missed in the pial layer after mri_segment
Hello-- We have a set of scans with bad artifact throughout the temporal lobe and the superior cortex. We've had to do the normalization steps (n3 correction, normalization) manually on most of these scans to preserve the gm/wm boundary. Now, when we run mri_segment, it leaves out some gray matter along the pial border. Is there a correction for this? Mri_segment has wlo and whi and ghi, but no glo, and it doesn't look like there's a method to add gray matter to the pial boundary like there is to remove it. Thank you, Erin Browning ___ 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] Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all
Hi, I have some trouble running recon-all longitudinal pipelines. When recon-all comes to mri_register_ca it crashes without giving a message, even tough 8g ram was available. I have run the program with -debug. Is there any other option I may use? The system is running Rocks 6.0 (Mamba), and it uses Slurm queue system. Can I use the FreeSurfer 5.3 longitudinal process with data processed with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed effects model MATLAB tools. 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] beta weights from FS-Fast analysis
I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] beta weights from FS-Fast analysis
then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with
Re: [Freesurfer] Q) Medial_wall.label
Hi Yune you are better off using the ?h.cortex.label file to mask in what is needed for each subject cheers Bruce On Wed, 17 Jul 2013, Yune Lee wrote: Hello freesurfer experts, For visualization purpose (i.e., displaying group maps), I applied a mask for medial wall regions using the files (e.g., rh.Medial_wall.label or lh.Medial.wall.label), which I found in fsaverage/label/ directory. However, I noticed a somewhat imperfect medial wall masking in both hemispheres, such that transversing lines are seen in unthresholded t maps for both hemispheres (see attached ). Those lines eventually disappear when I increased threshold, but I wonder why this happened. Any ideas? best, yune ___ 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] Gray matter missed in the pial layer after mri_segment
Hello Erin, Thank you so much for asking. I have been curious to know this, too. Sincerely, Ye On Wed, Jul 17, 2013 at 12:41 PM, Erin Browning brown...@uwm.edu wrote: Hello-- We have a set of scans with bad artifact throughout the temporal lobe and the superior cortex. We've had to do the normalization steps (n3 correction, normalization) manually on most of these scans to preserve the gm/wm boundary. Now, when we run mri_segment, it leaves out some gray matter along the pial border. Is there a correction for this? Mri_segment has wlo and whi and ghi, but no glo, and it doesn't look like there's a method to add gray matter to the pial boundary like there is to remove it. Thank you, Erin Browning ___ 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 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] beta weights from FS-Fast analysis
It's a boxcar design so 20.265. mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 17, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you ran mkanalysis-sess, what did you set --refeventdur to? On 07/17/2013 02:50 PM, Joseph Dien wrote: then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files
Re: [Freesurfer] beta weights from FS-Fast analysis
It's a little complicated. Basically there were eight runs, comprising four conditions (me, we, you1, you2) each with two adjoining runs. For the analysis, I merged each of the pairs into a single run and added a nuisance regressor to account for the difference in run means. There were a total of four different kinds of boxcars (AR, CS, EM, MP). So 4x4=16 conditions. There was also a covariate of non-interest to mark the switch point for each boxcar, one for each run, so 20 total. The 7 nuisance regressors are six movement covariates plus one to account for merging eight runs into four (it consists of 1 for the first half and -1 for the second, so the difference in the run means). I'm using the movement covariates from a prior SPM run since ARTdetect (for detecting bad volumes) isn't set up for AFNI style data. From all published accounts the different movement detection routines yield similar enough results that it shouldn't be a problem (consistent with what I found when I compared them for this dataset). You're thinking that collinearity could have reduced the effect sizes? When I correlate the X.X regressor matrix, the 20 predictors don't correlate by more than about .2 at worst. I do see greater correlations with some of the nuisance regressors (as high as the .4 range). Are my betas unusually small for FSFAST analyses? They did come up clusterwise significant at least. Or should I not worry? I'm not sure what to expect from FSFAST analyses. Thanks! Joe On Jul 17, 2013, at 3:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: why do you have 20 conditions? And what are the 7 nuisance regressors? On 07/17/2013 03:54 PM, Joseph Dien wrote: It's a boxcar design so 20.265. mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 17, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: when you ran mkanalysis-sess, what did you set --refeventdur to? On 07/17/2013 02:50 PM, Joseph Dien wrote: then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly
[Freesurfer] Cortical surface
Dear Freesurfer experts, I am interested in running cortical surface area on longitudinal data from MRI scans and run multisubject comparisons (patients vs controls). I would like to ask you where could I find either a tutorial or a guide for performing such analysis. Also I am not familiar with freesurfer, so I am not sure which type of preprocessing should be undertaken.I would greatly appreciate your valuable help on this topic.Pablo ___ 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] recon-all steps specified into volume and surface based stream?
Dear FreeSurfer experts, I was wondering if there is anywhere a table or hint, suggesting which particular steps of all the recon-all steps (i.e. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) are part of the volume-based or the surface-based stream or both? I also found this diagram https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllBlockDiagram but I'm unsure if the colours are supposed to give me any clues. I'm familiar with the broad processing stages of the two streams off course but would very much love to understand the details better :) Thank you very much for your help, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] beta weights from FS-Fast analysis
Oh, right, the nuisance regressors are given a separate regressor for each run. I had forgotten! On 07/17/2013 04:55 PM, Joseph Dien wrote: On Jul 17, 2013, at 4:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 07/17/2013 04:48 PM, Joseph Dien wrote: The single nuisance regressor models the difference between the merged runs. So if the first run had a mean of 90 and the second run had a mean of 110 then the merged run mean would be 100. The nuisance regressor has 1s for the volumes of the first run and -1s for the volumes of the second run so it ends up with a beta value of 10, thus accounting for the difference between these two sets of volumes. I think it does make sense. Do you do this in a single regressor? So you would have a +1 -1 pattern repeated 4 times? I think to make it work, you would need 4 regressors. In any event, FSFAST will do the right thing, so maybe it is not important. Looking at the X.X file, it did create four nuisance regressors. I'm really impressed with how well FSFAST handles all this! :) In any case, while it was necessary to do so for my original SPM analyses since it uses a separate covariates for each run, after working through the FSFAST procedures with your help I see that is not the case for FSFAST (a single regressor models a given condition in all the runs). I'll try doing as you suggest to see what difference it makes. It is indeed cognitive areas and the manipulations are subtle social cognition manipulations so perhaps not surprising after all. I'll send you the paradigm file separately. Thanks for taking the time to look into this! Joe On Jul 17, 2013, at 4:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is not necessary or beneficial to combine the runs in this way. FSFAST will do all this for you and keep account of all the runs and transitions. FSFAST will put in regressors to fit each of the run means. The single regressor you have is not the right way to hand this (at least I don't understand how it works). It could be that the low % signal change is related to the colinearity between the task waveform and the mean regressors. Can you set things up in the way that FSFAST expects them and don't use any nuisance regressors? Also, in what area are you looking at the percent change? .02% sounds very small, but may be if it is in some cognitive area, maybe it is ok. If it is in visual cortex, then it looks way too low. Also, can you send the paradigm file? doug On 07/17/2013 04:27 PM, Joseph Dien wrote: It's a little complicated. Basically there were eight runs, comprising four conditions (me, we, you1, you2) each with two adjoining runs. For the analysis, I merged each of the pairs into a single run and added a nuisance regressor to account for the difference in run means. There were a total of four different kinds of boxcars (AR, CS, EM, MP). So 4x4=16 conditions. There was also a covariate of non-interest to mark the switch point for each boxcar, one for each run, so 20 total. The 7 nuisance regressors are six movement covariates plus one to account for merging eight runs into four (it consists of 1 for the first half and -1 for the second, so the difference in the run means). I'm using the movement covariates from a prior SPM run since ARTdetect (for detecting bad volumes) isn't set up for AFNI style data. From all published accounts the different movement detection routines yield similar enough results that it shouldn't be a problem (consistent with what I found when I compared them for this dataset). You're thinking that collinearity could have reduced the effect sizes? When I correlate the X.X regressor matrix, the 20 predictors don't correlate by more than about .2 at worst. I do see greater correlations with some of the nuisance regressors (as high as the .4 range). Are my betas unusually small for FSFAST analyses? They did come up clusterwise significant at least. Or should I not worry? I'm not sure what to expect from FSFAST analyses. Thanks! Joe On Jul 17, 2013, at 3:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: why do you have 20 conditions? And what are the 7 nuisance regressors? On 07/17/2013 03:54 PM, Joseph Dien wrote: It's a boxcar design so 20.265. mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 17, 2013, at 3:50 PM, Douglas N Greve s. gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] Artefactual skull stripping for some subjects
Dear Bruce, Could you please let me know whether my message of last week, in which I uploaded the subject's volssurfs, have reached the list? I haven't received a reply about those questions and was wondering whether that email maybe got rejected due to the large size of the attachments. The questions should be visible in plaintext below, please let me know if I should upload the files on a sharing server Thanks! Tudor On 15 July 2013 19:51, Tudor Popescu tud...@gmail.com wrote: Hi again, I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions! Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu tud...@gmail.com wrote: Thanks Bruce. So the massive chunks that appear as missing in freeview, e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces don't exist there. If I mouse above that area, brainmask.mgz intensities (which seem to be always identical to T1.mgz ones) seem quite normal to me, i.e. they're not all 0 but vary in a range centred around ~100. As for the segmentation (aseg) - not quite sure where I need to look for that. I attach here the main volumes surfaces of this subject. Could my -wsthresh 35 recon not have replaced the existing one? Many thanks again! Tudor PS: why does freeview show the coordinates in the order [x z y] instead of [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle coordinate to decrease, rather than the third one. PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to do with conformity and intensity correction, just like the difference between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would be a binary image (a mask consisting of 0s and 1s), rather than a regular (skull-stripped) structural. On 11 July 2013 21:40, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tudor can you cc the list so others can answer? What are the intensities in the excluded right temporal wm in the brainmask.mgz? What is the aseg like there? Looks like an intensity normalization failure, but I'm not sure why. If you want to upload the subject I'll take a look Bruce On Thu, 11 Jul 2013, Tudor Popescu wrote: Hi Bruce, Sorry, wasn't sure whether you'd seen my previous message. So in the meantime, after the following command for subject C06 (whose artefactual skull strip I previously included as a screenshot) completed without error, recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06 ..the volumessurfaces still look bad (see screenshot and recon log attached). C06 is just one of several subjects for which this has happened. Is there anything else I can try? Thanks! Tudor On 9 July 2013 13:33, Tudor Popescu tud...@gmail.com wrote: Thanks for clarifying this Doug! Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: 001.mgz - raw.mgz - orig.mgz - nu.mgz - T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: Thanks Bruce. I have looked at that part of the wiki but I was wondering whether the screenshots at all suggest that all artefacts are likely to be the result of the same problem, and that e.g. re-running recon for all subjects with a watershed25 and with the -no-wsgcaatlas flag might be the thing to do in this case, rather than manually editing slices in tkmedit. So after making these corrections to all affected subjects, before proceeding to analyses, is a visual inspection in freeview of the brain.mgz of all subjects enough? It seems like some of these skull-stripping errors are quite subtle and can be easily missed (as I have, in fact, when I checked the output after my first recon-all). the T1.mgz is intensity corrected and conformed (the orig.mgz is just conformed). So are both derived from 001.mgz? Otherwise, what is the difference between 001.mgz and orig.mgz? Thanks! Tudor __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Artefactual skull stripping for some subjects
Hi Tudor, yes, it got through. It's on our list of things to get to, we just haven't gotten there yet Bruce On Wed, 17 Jul 2013, Tudor Popescu wrote: Dear Bruce, Could you please let me know whether my message of last week, in which I uploaded the subject's volssurfs, have reached the list? I haven't received a reply about those questions and was wondering whether that email maybe got rejected due to the large size of the attachments. The questions should be visible in plaintext below, please let me know if I should upload the files on a sharing server Thanks! Tudor On 15 July 2013 19:51, Tudor Popescu tud...@gmail.com wrote: Hi again, I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions! Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu tud...@gmail.com wrote: Thanks Bruce. So the massive chunks that appear as missing in freeview, e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces don't exist there. If I mouse above that area, brainmask.mgz intensities (which seem to be always identical to T1.mgz ones) seem quite normal to me, i.e. they're not all 0 but vary in a range centred around ~100. As for the segmentation (aseg) - not quite sure where I need to look for that. I attach here the main volumes surfaces of this subject. Could my -wsthresh 35 recon not have replaced the existing one? Many thanks again! Tudor PS: why does freeview show the coordinates in the order [x z y] instead of [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle coordinate to decrease, rather than the third one. PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to do with conformity and intensity correction, just like the difference between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would be a binary image (a mask consisting of 0s and 1s), rather than a regular (skull-stripped) structural. On 11 July 2013 21:40, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tudor can you cc the list so others can answer? What are the intensities in the excluded right temporal wm in the brainmask.mgz? What is the aseg like there? Looks like an intensity normalization failure, but I'm not sure why. If you want to upload the subject I'll take a look Bruce On Thu, 11 Jul 2013, Tudor Popescu wrote: Hi Bruce, Sorry, wasn't sure whether you'd seen my previous message. So in the meantime, after the following command for subject C06 (whose artefactual skull strip I previously included as a screenshot) completed without error, recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06 ..the volumessurfaces still look bad (see screenshot and recon log attached). C06 is just one of several subjects for which this has happened. Is there anything else I can try? Thanks! Tudor On 9 July 2013 13:33, Tudor Popescu tud...@gmail.com wrote: Thanks for clarifying this Doug! Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: 001.mgz - raw.mgz - orig.mgz - nu.mgz - T1.mgz If you only have
