[Freesurfer] converting .thickness files of T1 MRI from FreeSurfer into AFNI
Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media Please let me help me to solve this problem Thank you :) Best Regards, Muhammad Naveed Iqbal Qureshi ___ 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] brain orientation in qdec
Dear experts, I ran recon-all with qcache. When loading the right hemisphere of fsaverage (or any other surface reconstruction) into tksurfer (for example command: tksurfer fsaverage rh white), the left hemisphere surface is displayed, and it is upside down. When I import annotations they load in the same orientation as the surface. However, the coordinates and the labels, displayed in the Tksurfer Tools window, are not. For example, when I move the cursor to the temporal lobe, the label says it's postcentral. I do not mind manually turning the surfaces in tksurfer, but I do need to be sure I am looking at the correct hemispheres, coordinates and labels. I hope you can help me solve this. Thank you in advance. Best wishes, Lizanne ___ 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] converting .thickness files of T1 MRI from FreeSurfer into AFNI
Hi Muhammad try: set sdir=/home/naveed/freesurfer/subjects/CHR01/surf mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik cheers Bruce On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media Please let me help me to solve this problem Thank you :) Best Regards, Muhammad Naveed Iqbal Qureshi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all error
Hello Happy New Year! I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached. All the best throughout 2014! Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data recon1job.bash Description: Binary data ___ 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: Anatomical segmentation - question
it probably doesn't matter, but Doug is the Talairach expert, so perhaps he can comment Bruce On Mon, 6 Jan 2014, Rotem Saar wrote: Dear freesurfer experts, I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below – from some reason, the two images don't fit. Should I use scale brain ? I know this is not recommended thus want to consult with u first – Can u please comment on why this is happening? Is there any value that corresponds to how good is the segmentation ? if yes, where can I find it ? My script is written below. Thanks, Rotem Anatomical segmentation: first step- 23 hours: recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I1.dcm -s FOLDER-NAME second step:(gyrus=green, sulcus=red) tksurfer -curv FOLDER-NAME lh/rh inflated third step: (talairch registretion) tkmedit FOLDER-NAME brainmask.mgz File- transforms- load transform AUX- Browse- talairch.xfm forth step: (simetry - allows changing 12df transformation. if we made any changes we should click save reg and run this command again) tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig IF WE CHANGE ANYTHING, CLICK SAVE REG AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME fifth step: (scalp removal: if removed too much, rise up from the value 25: recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME to check the result press: tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white ) for hand correction: tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz tools- configure volume brush - MARK: mode=clone, source=Aux tools- configure brush info (for choosing brush size) click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing voxels : slice by slice. when finish, click: File- save main volume sisxt step: (cp for correcting segmentation) tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white seventh step: (done) recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel ___ 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] MNC label to Freesurfer
Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar ___ 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] MNC label to Freesurfer
Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar ___ 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] Are two T1 scans helpful for better recon-all?
Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list 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] MNC label to Freesurfer
Than you can use mri_binarize with the --match flag. --match matchval --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar 2014/1/6 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Are two T1 scans helpful for better recon-all?
Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list 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] Are two T1 scans helpful for better recon-all?
Thank you so much, Bruce. On Mon, Jan 6, 2014 at 3:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai 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] MNC label to Freesurfer
Hi Caspar can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject? cheers Bruce On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar 2014/1/6 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: recon-all exited w/errors
oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. How do I perform the alternative or manually tailarach? Thank you very much, Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors Hi Katica what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually. cheers Bruce On Thu, 2 Jan 2014, Boric, Katica A. wrote: Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST 2014 ___ 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
Re: [Freesurfer] MNC label to Freesurfer
Hi Bruce and Lilla, I have a MNC volume that contains area labels, ie voxels belonging to one label all have the same intensity value. I am trying to get this converted into Freesurfer label files for further analysis in volume space. Following Lilla's advice, I am first using mri_binarize with --match. I figured that I can then use mri_cor2label with --id 1 to get a label file from the binary mask, correct? There seem to be some individual voxels outside the labeled area that have the same values as the label; they are scattered across the volume. Is there a way to cluster size threshold the binarized mask? Thanks, Caspar 2014/1/6 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject? cheers Bruce On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar 2014/1/6 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FW: FW: recon-all exited w/errors
Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. How do I perform the alternative or manually tailarach? Thank you very much, Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors Hi Katica what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually. cheers Bruce On Thu, 2 Jan 2014, Boric, Katica A. wrote: Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST 2014
Re: [Freesurfer] FW: FW: recon-all exited w/errors
what is the slice thickness? Usually we recommend no dimension be thicker than 1.5mm or so On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. How do I perform the alternative or manually tailarach? Thank you very much, Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors Hi Katica what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually. cheers Bruce On Thu, 2 Jan 2014, Boric, Katica A. wrote: Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013
Re: [Freesurfer] FW: FW: recon-all exited w/errors
Its 1mm! But I found a newer study for the subject, so I will try this new one and if it still does not work, I will email back! Thanks so much again! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 4:27 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: recon-all exited w/errors what is the slice thickness? Usually we recommend no dimension be thicker than 1.5mm or so On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. How do I perform the alternative or manually tailarach? Thank you very much, Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors Hi Katica what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually. cheers Bruce On Thu, 2 Jan 2014, Boric, Katica A. wrote: Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform:
Re: [Freesurfer] FW: FW: recon-all exited w/errors
1mm and 60 slices covers the whole brain? Usually it requires more like 160 slices. On Mon, 6 Jan 2014, Boric, Katica A. wrote: Its 1mm! But I found a newer study for the subject, so I will try this new one and if it still does not work, I will email back! Thanks so much again! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 4:27 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: recon-all exited w/errors what is the slice thickness? Usually we recommend no dimension be thicker than 1.5mm or so On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: Hi Bruce! Thank you very much for your response! The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. How do I perform the alternative or manually tailarach? Thank you very much, Katica From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors Hi Katica what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually. cheers Bruce On Thu, 2 Jan 2014, Boric, Katica A. wrote: Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014
[Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon
Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ 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] Cannot run unpacksdcmdir on buckner_data/014-anon
Not sure. Try running mri_convert 001.dcm deleteme.mgh if it fails, capture the screen output and send it to the list doug On 01/06/2014 06:31 PM, Anders Olsen wrote: Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
