[Freesurfer] Fwd: pars triangular and BA44 segmentation bug?
Dear Bruce, Did you also identified a strong rightward asymmetry (with pars triangular and BA44) in your data analyzed by freesurfer 5.1? Just, to be sure, that this is not an issue only with our data. I'd like to use the TRACULA as well, and because tracula uses the cortical parcellation of our subjects I'm not sure that it is worth to start TRACULA now, or waiting for your cortical parcellation fix. Sorry for disturbing you again with the same issue, but it is very important for us to know, that it is a real issue with the cortical parcellation or we messed up something, and if it is a real issue, which labels we shouldn't use for statistical analysis. Thank you in advance for your answer, Gabor 2012/6/25 Bruce Fischl fis...@nmr.mgh.harvard.edu sure. Thanks for pointing out the BA44 issue. We'll put together a fix in the next couple of weeks Bruce On Mon, 25 Jun 2012, Gabor Perlaki wrote: Dear Bruce, I've checked the pars triangularis. It was right-lateralized in 79 subjects and left-lateralized in only 19 subjects. Thanks, Gabor 2012/6/23 Bruce Fischl fis...@nmr.mgh.harvard.edu the structures don't need a threshold. Do you know that pars triangularis is left lateralized? For the BAs will get you a solution On Sat, 23 Jun 2012, Gabor Perlaki wrote: Dear Bruce, We don't used any thresholding by ourselves, we just took BA44 volumes out of the text-file in the stats directory. Should we use thresholded values instead of the volumes reported by the text files in the stats directory? Could we use the volumes reported by the aparc.stats and aseg.stats files for any statistical analyses, or do we need threshold that structures as well? Thanks, Gabor 2012/6/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Gabor are you thresholding the BA4 label? In 5.2 we will distribute some tools to automatically threshold the labels so that the predicted area has the average area of the input labels. The right BA44 had more spatial spread than the left, so you might be including a lot of low probability vertices. cheers Bruce On Sat, 23 Jun 2012, Gabor Perlaki wrote: Dear Bruce, In the paper Left-right asymmetry in volume and number of neurons in adult Broca's area. by Katrin Amunts, 10 subjects (5 men and 5 women) were studied, and the volume of BA44 was greater in the left hemisphere than in the right in all ten cases. So, it is very strange that the volume of BA44 was greater in the right hemisphere in all of the 80 subjects analyzed by Eniko. Thanks, Gabor 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.
[Freesurfer] annot 2 label file conversion
Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) arnaud.me...@imed.jussieu.fr http://www.imed.jussieu.fr ___ 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] annot 2 surf
Dear all, There is a way to convert annot file into surface? -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) arnaud.me...@imed.jussieu.fr http://www.imed.jussieu.fr ___ 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] Clusterwise correction for multiple comparisons
Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed ___ 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] fsgd file
Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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] Fwd: pars triangular and BA44 segmentation bug?
Hi Gabor, I actually don't know, but I think Anastasia has a fix for the thresholding issue. cheers Bruce On Wed, 11 Jul 2012, Gabor Perlaki wrote: Dear Bruce, Did you also identified a strong rightward asymmetry (with pars triangular and BA44) in your data analyzed by freesurfer 5.1? Just, to be sure, that this is not an issue only with our data. I'd like to use the TRACULA as well, and because tracula uses the cortical parcellation of our subjects I'm not sure that it is worth to start TRACULA now, or waiting for your cortical parcellation fix. Sorry for disturbing you again with the same issue, but it is very important for us to know, that it is a real issue with the cortical parcellation or we messed up something, and if it is a real issue, which labels we shouldn't use for statistical analysis. Thank you in advance for your answer, Gabor 2012/6/25 Bruce Fischl fis...@nmr.mgh.harvard.edu sure. Thanks for pointing out the BA44 issue. We'll put together a fix in the next couple of weeks Bruce On Mon, 25 Jun 2012, Gabor Perlaki wrote: Dear Bruce, I've checked the pars triangularis. It was right-lateralized in 79 subjects and left-lateralized in only 19 subjects. Thanks, Gabor 2012/6/23 Bruce Fischl fis...@nmr.mgh.harvard.edu the structures don't need a threshold. Do you know that pars triangularis is left lateralized? For the BAs will get you a solution On Sat, 23 Jun 2012, Gabor Perlaki wrote: Dear Bruce, We don't used any thresholding by ourselves, we just took BA44 volumes out of the text-file in the stats directory. Should we use thresholded values instead of the volumes reported by the text files in the stats directory? Could we use the volumes reported by the aparc.stats and aseg.stats files for any statistical analyses, or do we need threshold that structures as well? Thanks, Gabor 2012/6/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Gabor are you thresholding the BA4 label? In 5.2 we will distribute some tools to automatically threshold the labels so that the predicted area has the average area of the input labels. The right BA44 had more spatial spread than the left, so you might be including a lot of low probability vertices. cheers Bruce On Sat, 23 Jun 2012, Gabor Perlaki wrote: Dear Bruce, In the paper Left-right asymmetry in volume and number of neurons in adult Broca's area. by Katrin Amunts, 10 subjects (5 men and 5 women) were studied, and the volume of BA44 was greater in the left hemisphere than in the right in all ten cases. So, it is very strange that the volume of BA44 was greater in the right hemisphere in all of the 80 subjects analyzed by Eniko. Thanks, Gabor 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
Re: [Freesurfer] annot 2 label file conversion
Hi Arnaud this question may need to wait for Doug to return. If you don't get an answer in a couple of days try reposting, and please include your exact command line and screen output and FS version. cheers Bruce On Wed, 11 Jul 2012, Arnaud Messé wrote: Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, ___ 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] annot 2 surf
Hi Arnaud no, although I'm not even sure what you mean. Annot files contain a label value for every vertex location but no information on where in space it should be or what it's neighbors are. cheers Bruce On Wed, 11 Jul 2012, Arnaud Messé wrote: Dear all, There is a way to convert annot file into surface? ___ 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] cortical thickness and ICA of resting state fMRI
Hi all, I was wondering if anyone knows about any articles that compare/relate cortical thickness analysis with resting state ICA results? More specifically, I'm looking for articles that study cortical thickness changes in different regions of brain and its possible relation to group clusters found using ICA analysis of resting state fMRI. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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] ROI functional anatomical cross
Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that would cross the group level map with each cortical structure generated by freesurfer's recon-all? Thanks. ___ 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] error message for recon-all
Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/and with $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 # #@# MotionCor Wed Jul 11 17:54:17 CEST 2012 ERROR: no run data found in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz mkdir: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory cp: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory cat: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory. Thank you very much in advance and greetings from Oslo, Muriel Bruchhage ___ 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
Re: [Freesurfer] error message for recon-all
Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/ andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 _3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 # #@# MotionCor Wed Jul 11 17:54:17 CEST 2012 ERROR: no run data found in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz mkdir:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory cp:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ scripts/build-stamp.txt: Not a directory cat:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory. Thank you very much in advance and greetings from Oslo, Muriel Bruchhage ___ 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.
Re: [Freesurfer] slanted
Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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] slanted
Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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] slanted
You can either upload it to our ftp server or use the email file drop system. See link below for details. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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] slanted
Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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] slanted
i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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] slanted
when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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] slanted
oh i'm trying to do the e-mail file drop though, that's fine too right? i'm just not sure what e-mail to use for the recipient e-mail. From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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] slanted
can i just send it to freesurfer@nmr.mgh.harvard.edu? thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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] slanted
No! Do you have a dropbox account? Copy there and send the link to them. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Jul 11, 2012 at 3:39 PM, Borzello, Mia mborze...@partners.orgwrote: can i just send it to freesurfer@nmr.mgh.harvard.edu? thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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
Re: [Freesurfer] slanted
oh, you can give mine if you want On Wed, 11 Jul 2012, Borzello, Mia wrote: oh i'm trying to do the e-mail file drop though, that's fine too right? i'm just not sure what e-mail to use for the recipient e-mail. From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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] slanted
no! Don't do that - just use mine On Wed, 11 Jul 2012, Borzello, Mia wrote: can i just send it to freesurfer@nmr.mgh.harvard.edu? thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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.
[Freesurfer] the make_average_subject without aparc.annot
Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig ___ 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] the make_average_subject without aparc.annot
Doug is away so it may be a couple of days until he answers... On Wed, 11 Jul 2012, Leon wrote: Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_ surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig ___ 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] error message for recon-all
It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 _3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin
Re: [Freesurfer] error message for recon-all
sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 _3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13
Re: [Freesurfer] Combining linear transformations
Hi Martin,
Thanks for the suggestion. I resolved the issue by using the --regheader
flag in tkmregister, and --reg as the default output by mri_vol2vol (even
though I did supply a reg-final flag). It seems like I mixed up the
difference between reg-final and the default registration matrix. would you
mind explaining the difference? in any event, here is my script:
for i in $(ls posterior_left_* posterior_Left-Hippocampus.mgz
posterior_right_* posterior_Right-Hippocampus.mgz); do
fname=$(basename $i); fname=${fname%%.*};
echo $fname
tkregister2 --noedit --reg hc_subfields/xfm_$fname.mgz.reg --regheader
--targ nu.mgz --mov $i --ltaout hc_subfields/xfm_$fname.lta
mri_concatenate_lta hc_subfields/xfm_$fname.lta xfm_nu_to_pre.lta
hc_subfields/xfm_$fname_to_pregado.lta
mri_convert -at hc_subfields/xfm_$fname_to_pregado.lta $i
hc_subfields/final/final_$fname.mgz;
done
Thanks,
Usman
On Jul 10, 2012, at 10:40 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Usman ,
Try validating each step by applying each transform. I usually use
mri_convert -at
For it.
Best Martin
Usman Khan us...@bwh.harvard.edu wrote:
Hi Martin,
Thanks for the quick reply. I tried the following commands, but it looks
like the volumes are still out of line. Is there something I am missing?
to get from hc_subfield -- nu.mgz -- t1_cbv
#register and create transforms
1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final *
xfm_hcsubfield_to_nu.dat* --regheader
2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta *xfm_nu_to_t1.lta
* --satit
#convert output from (1) from reg-final.dat to .lta
3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg
*xfm_hcsubfield_to_nu.dat
--ltaout test.lta*
4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta *final.lta*
#apply lta file, using t1_cbv as target and hc_subfield as --mov file
5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg *final.lta* --out
test.mgz
On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
Hi Usman,
you need to convert the reg to lta (using tkregister2) and then you can
use mri_concatenate_lta .
Cheers, Martin
On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
Hi FreeSurfer,
I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
(0.682x0.682x3mm) image used for CBV mapping. We have run FS, with
hippocampal subfields on the MPRAGE and would now like to transform
the posterior probability maps to the T1-weighted CBV space.
I have been using
1) mri_vol2vol with --regheader to map the posterior_* subfield files
to nu.mgz space
2) mri_robust_register to coregister the nu.mgz file to the
T1-weighted CBV image
Is there any way to combine the .reg and .lta files from (1) and (2)
to transform the subfield posterior probability maps directly from
their 0.5mm^3 space to the T1-weighted CBV space? I have been
reluctant to create an intermediate volume between steps 1 and 2, as
resampling the subfield probability maps into 1x1x1mm nu.mgz space
will result in loss of resolution to the 0.68x0.68 (coronal) space in
the T1-weighted CBV scan.
Any help would be appreciated
Usman
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Re: [Freesurfer] error message for recon-all
Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 _3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find
Re: [Freesurfer] error message for recon-all
oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i path to dicom cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 _3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75
Re: [Freesurfer] Combining linear transformations
Hi Usman,
I'm an not very familiar with mri_vol2vol , maybe Doug knows the
difference between --reg and --reg-final. I would also expect it to give
the same result in your case (as you don't apply any manual --rot or
--trans).
Anyway, happy you got it working.
Best, Martin
On Wed, 2012-07-11 at 16:46 -0400, Usman Khan wrote:
Hi Martin,
Thanks for the suggestion. I resolved the issue by using the
--regheader flag in tkmregister, and --reg as the default output by
mri_vol2vol (even though I did supply a reg-final flag). It seems like
I mixed up the difference between reg-final and the default
registration matrix. would you mind explaining the difference? in any
event, here is my script:
for i in $(ls posterior_left_* posterior_Left-Hippocampus.mgz
posterior_right_* posterior_Right-Hippocampus.mgz); do
fname=$(basename $i); fname=${fname%%.*};
echo $fname
tkregister2 --noedit --reg hc_subfields/xfm_$fname.mgz.reg
--regheader --targ nu.mgz --mov $i --ltaout
hc_subfields/xfm_$fname.lta
mri_concatenate_lta hc_subfields/xfm_$fname.lta xfm_nu_to_pre.lta
hc_subfields/xfm_$fname_to_pregado.lta
mri_convert -at hc_subfields/xfm_$fname_to_pregado.lta $i
hc_subfields/final/final_$fname.mgz;
done
Thanks,
Usman
On Jul 10, 2012, at 10:40 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu wrote:
Hi Usman ,
Try validating each step by applying each transform. I usually use
mri_convert -at
For it.
Best Martin
Usman Khan us...@bwh.harvard.edu wrote:
Hi Martin,
Thanks for the quick reply. I tried the following commands, but it
looks like the volumes are still out of line. Is there something I
am missing?
to get from hc_subfield -- nu.mgz -- t1_cbv
#register and create transforms
1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final
xfm_hcsubfield_to_nu.dat --regheader
2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta
xfm_nu_to_t1.lta --satit
#convert output from (1) from reg-final.dat to .lta
3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz
--reg xfm_hcsubfield_to_nu.dat --ltaout test.lta
4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta final.lta
#apply lta file, using t1_cbv as target and hc_subfield as --mov
file
5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg final.lta
--out test.mgz
On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu wrote:
Hi Usman,
you need to convert the reg to lta (using tkregister2) and
then you can
use mri_concatenate_lta .
Cheers, Martin
On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
Hi FreeSurfer,
I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
(0.682x0.682x3mm) image used for CBV mapping. We have run
FS, with
hippocampal subfields on the MPRAGE and would now like to
transform
the posterior probability maps to the T1-weighted CBV
space.
I have been using
1) mri_vol2vol with --regheader to map the posterior_*
subfield files
to nu.mgz space
2) mri_robust_register to coregister the nu.mgz file to
the
T1-weighted CBV image
Is there any way to combine the .reg and .lta files from
(1) and (2)
to transform the subfield posterior probability maps
directly from
their 0.5mm^3 space to the T1-weighted CBV space? I have
been
reluctant to create an intermediate volume between steps 1
and 2, as
resampling the subfield probability maps into 1x1x1mm
nu.mgz space
will result in loss of resolution to the 0.68x0.68
(coronal) space in
the T1-weighted CBV scan.
Any help would be appreciated
Usman
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Re: [Freesurfer] the make_average_subject without aparc.annot
Hi, Bruce Thanks for the information. I can wait for his information after he comes back. Best Leon From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Wednesday, July 11, 2012 4:23 PM Subject: Re: [Freesurfer] the make_average_subject without aparc.annot Doug is away so it may be a couple of days until he answers... On Wed, 11 Jul 2012, Leon wrote: Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_ surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig ___ 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] error message for recon-all
Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: I added the -all at the end and skipped the -i flag, but I still get an error message: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz has 2 frames I am so sorry to bother you with these probably very amateur questions - but how can I have multiple frames when I just got one .mgz file and just one T1? Best, Muriel On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i path to dicom cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv
Re: [Freesurfer] error message for recon-all
Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: I added the -all at the end and skipped the -i flag, but I still get an error message: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz has 2 frames I am so sorry to bother you with these probably very amateur questions - but how can I have multiple frames when I just got one .mgz file and just one T1? Best, Muriel On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i path to dicom cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert first dicom.dcm
Re: [Freesurfer] error message for recon-all
you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look. On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: I added the -all at the end and skipped the -i flag, but I still get an error message: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz has 2 frames I am so sorry to bother you with these probably very amateur questions - but how can I have multiple frames when I just got one .mgz file and just one T1? Best, Muriel On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i path to dicom cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you very much in advance for all your help! Best, Muriel On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i path to dicom file. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source
[Freesurfer] Using bet with Freesurfer
Hello, We're working with a pediatric data set and have found that Freesurfer's skullstripping process is inadequate for our purposes. We're interested in using FSL's bet, which we have found to do a better job of skullstripping, in combination with the other steps of Freesurfer. In a previous email, Bruce recommended that the best way to do this would be to replace the watershed step with bet. How would we go about doing that while still obtaining the brainmask.mgz necessary for the rest of the stream? We've unsuccessfully tried using bet at different points in the stream. When using bet prior to initiating the Freesurfer stream, we've found that the Talairach transform is irreparably bad (leading to a severely altered ICV). We have also encountered difficulties when using bet on the skullstripped brainmask.mgz. So, we think that replacing Freesurfer's skullstrip with bet is the option, but we are unsure about how to proceed. Thank you for your help, Heather ___ 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] Using bet with Freesurfer
Hi Heather I guess you could run autorecon1, then run BET if the results are not satisfactors to replace the brainmask.mgz, then run autorecon2 and 3. cheers Bruce On Wed, 11 Jul 2012, Lugar, Heather wrote: Hello, We?re working with a pediatric data set and have found that Freesurfer?s skullstripping process is inadequate for our purposes. We?re interested in using FSL?s bet, which we have found to do a better job of skullstripping, in combination with the other steps of Freesurfer. In a previous email, Bruce recommended that the best way to do this would be to replace the watershed step with bet. How would we go about doing that while still obtaining the brainmask.mgz necessary for the rest of the stream? We?ve unsuccessfully tried using bet at different points in the stream. When using bet prior to initiating the Freesurfer stream, we?ve found that the Talairach transform is irreparably bad (leading to a severely altered ICV). We have also encountered difficulties when using bet on the skullstripped brainmask.mgz. So, we think that replacing Freesurfer?s skullstrip with bet is the option, but we are unsure about how to proceed. Thank you for your help, Heather ___ 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.
