Re: [Freesurfer] Calculate WM, GM and CSF volume
Hi Bruce, Yes, I would like to reduce the required calculation time, until desired results are available. Best regards, Iven -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 20. Juli 2011 15:19 An: Fellhauer, Iven Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Calculate WM, GM and CSF volume Hi Iven, is there a reason you don't want to just run recon-all -all? It's more time for the computer, but no more for you and will give you a lot more measures cheers Bruce On Wed, 20 Jul 2011, Fellhauer, Iven wrote: Dear All, I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta -calabel -segstatts -subject subject Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? Best regards, Iven Fellhauer ___ 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] Defining the Calcarine and distances from it in the Hinds et al. V1 label
Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I have a couple of questions: 1) Is it possible to automatically label just the calcarine itself? I know there is a pericalcarine label, but I am hoping to essentially label the line of the calcarine itself. 2) Is it possible to automatically find the occipital pole of the calcarine? The reason I want to do this is that it would then enable me to calculate the distance down the calcarine and the lateral distance away from the calcarine for each patch in the Hinds-V1 label. That potentially could be really useful in terms of sub-dividing the Hinds label into foveal and eccentric zones (although without retinotopy individual differences in M-scaling, for example, might limit interpretability). Would mris_divide_parcellation be useful here? Thanks in advance, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : sing...@cardiff.ac.uk ___ 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] Pial Edits on Base Template
Hi Jeff, I think you'll have to run with -force. In the newer version 5.1, this is updated so that you don't have to anymore. And you might be right that deleting the folder is not a good idea since the edits were made in there. If you made edits in the cross and want to rerun the base, then you can either do -force or delete the folder or delete whichever file you made edits on (if made edits on wm.mgz in cross, delete wm.mgz in base). Martin, is that correct? -Khoa On Wed, 20 Jul 2011, Jeff Sadino wrote: Hello, I have a subject with three timepoints I am putting through the longitudinal stream in fs 5.0.0. After the base template was created, I edited some of the pial surfaces on the base. Now when I run the command: recon-all -base subject -autorecon2-pial -autorecon3, it says: ERROR: /mnt/fs5/050079 exists, delete or re-run with -force This is confusing to me because if I delete the folder, then wont my edits also be deleted? I ran it using the force flag, and it seems to be going ok. I just want to ask if this is the best way to do this. Thank you, Jeff Sadino ___ 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] Tracula with individual bvecs files
Hi Jürgen - There is no bvecslist option. Currently there is no support for multiple bvecs files in one configuration file but it's certainly something that can be added to the next release. For now you'd have to change the configuration file accordingly for each subject with a different bvecs file. Or I could make the change now and send you a patched version of the trac-* scripts, since it's something potentially useful to a lot of people and not major :) a.y On Thu, 21 Jul 2011, Jürgen Hänggi wrote: Dear FS and Tracula experts Because of correction for slice angulation during scanning, I have as many bvecs files as subjects. Therefore I created a list for the bvecs set bvecslist = (b101/bvecs b102/bvecs) but tracula reports the following error: mv: rename /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/dwi_orig_flip.mghdti .bvecs to /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/bvecs: No such file or directory However, when using set bvecsfile, everthing works fine. Any idea how to deal with more than one bvecs file? Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] Calculate WM, GM and CSF volume
Hi Iven we don't recommend that as many steps interact. For example, although we don't do it automatically now, we do have procedures for automatically correcting the aseg based on the subsequently created surfaces. cheers Bruce On Thu, 21 Jul 2011, Fellhauer, Iven wrote: Hi Bruce, Yes, I would like to reduce the required calculation time, until desired results are available. Best regards, Iven -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 20. Juli 2011 15:19 An: Fellhauer, Iven Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Calculate WM, GM and CSF volume Hi Iven, is there a reason you don't want to just run recon-all -all? It's more time for the computer, but no more for you and will give you a lot more measures cheers Bruce On Wed, 20 Jul 2011, Fellhauer, Iven wrote: Dear All, I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta -calabel -segstatts -subject subject Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? Best regards, Iven Fellhauer ___ 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 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] Defining the Calcarine and distances from it in the Hinds et al. V1 label
Hi Krish, 1. What do you mean just the calcarine itself? Do you mean the fundus? mris_divide_parcellation can be used to chop the pericalcarine or V1 labels up along it's primary eigenaxis, which is a reasonable approximation to eccentricity. 2. You could draw occipital pole in fsaverage and use mri_label2label to map it to individuals. Not sure how well that works though as I've never tried it. cheers Bruce On Thu, 21 Jul 2011, Krish Singh wrote: Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I have a couple of questions: 1) Is it possible to automatically label just the calcarine itself? I know there is a pericalcarine label, but I am hoping to essentially label the line of the calcarine itself. 2) Is it possible to automatically find the occipital pole of the calcarine? The reason I want to do this is that it would then enable me to calculate the distance down the calcarine and the lateral distance away from the calcarine for each patch in the Hinds-V1 label. That potentially could be really useful in terms of sub-dividing the Hinds label into foveal and eccentric zones (although without retinotopy individual differences in M-scaling, for example, might limit interpretability). Would mris_divide_parcellation be useful here? Thanks in advance, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : sing...@cardiff.ac.uk ___ 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] Cortical segmentation error
Hi Bruce, thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this. About the heterotopias, is a good output to have someones classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not? Best regards, Carolina 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Carolina, it looks mostly to me like the surfaces are in the right place (the yellow and red lines). Don't look at the colored overlay - that is the aseg voxel segmentation and not what we typically use for cortical morphometry. Only look at the yellow and red lines. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: tiff I guess, I took the pictures from FS 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu what format are the files in the archive in? They don't have an extension On Tue, 19 Jul 2011, Carolina Valencia wrote: I hope this attachement works.I also noticed that some heterotopias are classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not. Best regards, Carolina 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Carolina, can you gzip it or use compression? Usually people can send a few images to the list. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: Dear FS experts, I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some GM not classified (empty color)) I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of ~700kb? Thanks a lot, Carolina 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. ___ 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] dcm conversion to nii
Hi Antonella, for each acquisition you give mri_convert *one* dicom file in that series and it will figure out the rest. You will then have one volume file per series. Something like: mri_convert one .dcm file in the Ax_PD series) Ax_PD.nii.gz cheers Bruce On Thu, 21 Jul 2011, Antonella Kis wrote: Good morning Bruce, Thank you for your answer and yes, I am posting my question to the list. For all my other subjects I had the MRI data converted by somebody else into one file .nii.gz for each subject. My question is how I can convert the MRI data (.dcm) for a new subject in a .nii.gz file? I have multiple file from MRI: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32 each of them containing lots of .dcm files. Do I need to convert all of them? If I give mri_convert one slice in each dicom series and convert each one to it's own volume how I can further use this data? Do I get an .nii.gz for each dicom file? I attached a type of file .nii.gz from another subject so you can see what type of files I need to get by conversion. Thank you very much. Antonella From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Sent: Wednesday, July 20, 2011 4:12 PM Subject: Re: dcm conversion to nii Hi Antonella can you post this type of question to the list so others can answer? I don't think you want them in one file as they probably have different resolution etc... Give mri_convert one slice in each dicom series and convert each one to it's own volume. cheers Bruce On Wed, 20 Jul 2011, Antonella Kis wrote: Dear Bruce, I have the MRI data (.dcm) for my subject p27 within the following files: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32. I would like to convert this data into one file.nii.gz. It will be correct if I will run: mri_convert p27 NPI027.nii.gz? Will FS know to convert based on this statement all my dcm files into one nii.gz file? If not how should I do it? Many thanks. Antonella 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] Cortical segmentation error
Hi Carolina, no, the aseg cortex/wm is not used for thickness or volume (it can be, but we don't recommend it). The surfaces are. As for the heterotopias, I don't really know what a good output would be. It depends what you want to do with them. I guess they should be gray matter, no? Bruce On Thu, 21 Jul 2011, Carolina Valencia wrote: Hi Bruce,thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this. About the heterotopias, is a good output to have someones classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not? Best regards, Carolina 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Carolina, it looks mostly to me like the surfaces are in the right place (the yellow and red lines). Don't look at the colored overlay - that is the aseg voxel segmentation and not what we typically use for cortical morphometry. Only look at the yellow and red lines. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: tiff I guess, I took the pictures from FS 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu what format are the files in the archive in? They don't have an extension On Tue, 19 Jul 2011, Carolina Valencia wrote: I hope this attachement works.I also noticed that some heterotopias are classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not. Best regards, Carolina 2011/7/19 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Carolina, can you gzip it or use compression? Usually people can send a few images to the list. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: Dear FS experts, I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some GM not classified (empty color)) I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of ~700kb? Thanks a lot, Carolina 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.
[Freesurfer] literature about multiple comparison correction
Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja. ___ 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] literature about multiple comparison correction
Check out hayasaka and nichols 2003. pdf below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf doug Tetiana Dadakova wrote: Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja. ___ 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.
Re: [Freesurfer] literature about multiple comparison correction
That paper is great. Lazar also has a nice review of a number of approaches in her book: Lazar, N. The statistical analysis of functional MRI data. On 7/21/11 11:39 AM, Douglas N Greve wrote: Check out hayasaka and nichols 2003. pdf below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf doug Tetiana Dadakova wrote: Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick ___ 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] Segmentation Fault during mri_ca_normalize
Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through mri_ca_normalize (error message below) - any ideas?? Thanks! Tali Swisher #@# CA Normalize Thu Jul 21 12:25:47 EDT 2011 /home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 -- 107 resetting gm mean[0]: 64 -- 64 input volume #1 is the most T1-like using real data threshold=19.0 using (122, 88, 141) as brain centroid... mean wm in atlas = 107, using box (106,72,120) -- (137, 104,162) to find MRI wm before smoothing, mri peak at 215 after smoothing, mri peak at 214, scaling input intensities by 0.500 scaling channel 0 by 0.5 using 244171 sample points... INFO: compute sample coordinates transform 1.134 0.005 0.006 -38.602; 0.006 1.132 0.138 -19.653; 0.004 -0.150 1.048 -20.038; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 41584 control points for structure... bounding box (142, 46, 61) -- (202, 147, 218) Left_Cerebral_White_Matter: limiting intensities to 97.0 -- 111.0 19 of 76 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter found 40735 control points for structure... bounding box (87, 48, 60) -- (144, 148, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 -- 107.0 27 of 73 (37.0%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3012 control points for structure... bounding box (146, 122, 85) -- (188, 161, 136) Left_Cerebellum_White_Matter: limiting intensities to 92.0 -- 105.0 5 of 18 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2764 control points for structure... bounding box (103, 122, 83) -- (144, 160, 137) Right_Cerebellum_White_Matter: limiting intensities to 95.0 -- 108.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem found 3520 control points for structure... bounding box (130, 115, 118) -- (158, 176, 147) Segmentation fault Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011 -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150 ___ 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] Segmentation Fault during mri_ca_normalize
Hi Tali can you email me the nu.mgz, the talairach.lta and the brainmask.mgz? I'll see if I can get it to happen and fix it. thanks Bruce On Thu, 21 Jul 2011, Tali Swisher wrote: Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through mri_ca_normalize (error message below) - any ideas?? Thanks! Tali Swisher #@# CA Normalize Thu Jul 21 12:25:47 EDT 2011 /home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 -- 107 resetting gm mean[0]: 64 -- 64 input volume #1 is the most T1-like using real data threshold=19.0 using (122, 88, 141) as brain centroid... mean wm in atlas = 107, using box (106,72,120) -- (137, 104,162) to find MRI wm before smoothing, mri peak at 215 after smoothing, mri peak at 214, scaling input intensities by 0.500 scaling channel 0 by 0.5 using 244171 sample points... INFO: compute sample coordinates transform 1.134 0.005 0.006 -38.602; 0.006 1.132 0.138 -19.653; 0.004 -0.150 1.048 -20.038; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 41584 control points for structure... bounding box (142, 46, 61) -- (202, 147, 218) Left_Cerebral_White_Matter: limiting intensities to 97.0 -- 111.0 19 of 76 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter found 40735 control points for structure... bounding box (87, 48, 60) -- (144, 148, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 -- 107.0 27 of 73 (37.0%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3012 control points for structure... bounding box (146, 122, 85) -- (188, 161, 136) Left_Cerebellum_White_Matter: limiting intensities to 92.0 -- 105.0 5 of 18 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2764 control points for structure... bounding box (103, 122, 83) -- (144, 160, 137) Right_Cerebellum_White_Matter: limiting intensities to 95.0 -- 108.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem found 3520 control points for structure... bounding box (130, 115, 118) -- (158, 176, 147) Segmentation fault Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011 -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150 ___ 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] Problem registering labels to native space
Quick update: this fix worked brilliantly.
Many thanks for the help,
J Richey
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 5:20 PM
To: John Richey
Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Problem registering labels to native space
In that case, try this instead
doug
# Create a register.dat to fsaverage/mni305 cd $SUBJECTS_DIR/subject/mri
tkregister2 --s subject --targ orig.mgz \
--ixfm transforms/talairach.xfm --zero-cras \
--reg transforms/talairach.reg.dat \
--mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz \
--noedit
# Create a register.dat to the 2mm version of fsaverage/mni305
mri_matrix_multiply \
-im $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.dat \
-im transforms/talairach.reg.dat \
-om transforms/mni305.2mm.reg.dat
# Check
tkregister2 --reg transforms/mni305.2mm.reg.dat \
--mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/orig.mgz \
--surfs
# Run label2label
mri_label2label --srclabel mni305.2mm.label \
--trglabel $SUBJECTS_DIR/subject/labels/mni305.2mm.label \
--regmethod volume \
--reg $SUBJECTS_DIR/subject/mri/transforms/mni305.2mm.reg.dat \
--xfm-invert
John Richey wrote:
Hi Doug, this is indeed an fsfast analysis. I used the fsaverage
subject included with the 5.1 distribution. Here is the code that I
used to produce the registration matrix for one subject. Note that I
did use mri_convert to change the .mgz files into .nii.gz
The use of flirt (below) is more of an ad-hoc solution to register
each subject's anatomical image to fsaverage. I'm not wedded to this
method if there's a better alternative.
bet ${SUBJECTS_DIR}/${SUBJECT}/mri/nu.nii.gz \
${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -f 0.3 -g 0
flirt -in ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -ref
${SUBJECTS_DIR}/fsaverage/mri/brain.nii.gz \ -out
${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.nii.gz \ -omat
${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.mat \ -bins 256 -cost
corratio -searchrx -90 90 -searchry -90 90 \ -searchrz -90 90 -dof 12
-interp trilinear
cd $SUBJECTS_DIR
tkregister2 --targ $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.nii.gz \
--mov $SUBJECTS_DIR/fsaverage/mri/brain.nii.gz \ --fsl
$SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.mat \ --reg
$SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.dat \ --noedit
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 3:11 PM
To: John Richey
Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Problem registering labels to native space
How did you create it? What is the actual fsaverage space? Is this
an FSFAST analysis?
doug
John Richey wrote:
Hi Doug, the .dat file that I mention below had already been
converted
into
a fs matrix using tkregister2.
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 12:38 PM
To: John Richey
Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Problem registering labels to native space
You can't use a flirt matrix with mri_label2label. You can convert a
flirt matrix to the proper format with tkregister2 using the --fsl
option (this will allow you to check the reg as well).
doug
John Richey wrote:
Hi Bruce,
The labels that I have fsaverage space are 3D/volume-based and not
surface-based labels.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 12:00 PM
To: John Richey
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] Problem registering labels to native space
Hi John
why are you using an affine volume registration for fsaverage? Why
not use surface registration?
Bruce
On Mon, 18 Jul 2011, John Richey wrote:
Hi Bruce - thanks for the reply.
Here is my command line:
mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT}
--srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \
--trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \
--regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat
Where brain_reg.dat is the subject-specific matrix I created
through FLIRT. However, as I mentioned, disincluding this matrix
does not seem to change the result much.
One other problem I encounter... Occasionally when I view the
label in native space, the label itself seems to be eroded on a
voxel-wise
basis.
That is, the label essentially appears as a series of
non-contiguous dots (which if dialated would become contiguous).
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 11:20 AM
To: John Richey
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Problem
[Freesurfer] long_mris_slopes error
I received the follow error while running a set of subjects under 'long_mris_slopes,' and wasn't able to decipher the problem. It appears that mris_calc is not able to do the division for these files (dividing by 0 perhaps?). Any help appreciated, here's the command and tail end of output/error, thanks. -Derin long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time scan_interval --qcache fsaverage === SUBJECT CH1840 fwhm 0 computing SPC mris_calc -o /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh ERROR 1 : mris_calc compute sym. pct. change (spc) problem? ___ 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] trac-all -bedp error
Hi, I run the trac-all bedp process and it comes up with the following errors: 56 slices processed 56 slices processed 57 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/stable5_1_0/bin/bedpostx_seychelles: line 281: kill: (12876) - No such process When I look at the processed data in dmri.bedpostx, I couldn't identify the problem. Kindly help. Phoebe. -- ___ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 pho...@nmr.mgh.harvard.edu ___ 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] trac-all -bedp error
Where is the data? On Thu, 21 Jul 2011, pho...@nmr.mgh.harvard.edu wrote: Hi, I run the trac-all bedp process and it comes up with the following errors: 56 slices processed 56 slices processed 57 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/stable5_1_0/bin/bedpostx_seychelles: line 281: kill: (12876) - No such process When I look at the processed data in dmri.bedpostx, I couldn't identify the problem. Kindly help. Phoebe. ___ 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.
