[Freesurfer] Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
Post-Doctoral applications are invited in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (narly.golest...@unige.ch). Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: narly.golest...@unige.ch. ___ 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] Chunks of missing WM
We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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 -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@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.
[Freesurfer] Beta maps
Dear FreeSurfer List, How can I visualise the beta maps ? previously there is a mail about this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html The /average7/ subject is missing in FreeSurfer 5.1, so I guess using /fsaverage/ is the same, but that command shows no results. The command: /tksurfer fsaverage lh inflated -overlay beta.mgh -fthresh 0 /shows red areas on blue cortex. Is this correct ? Thanks, Alex. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Beta maps
that command is correct. you might try adjusting the threshold doug On 12/14/2012 12:04 PM, Alex Hanganu wrote: Dear FreeSurfer List, How can I visualise the beta maps ? previously there is a mail about this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html The /average7/ subject is missing in FreeSurfer 5.1, so I guess using /fsaverage/ is the same, but that command shows no results. The command: /tksurfer fsaverage lh inflated -overlay beta.mgh -fthresh 0 /shows red areas on blue cortex. Is this correct ? Thanks, Alex. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Chunks of missing WM
Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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 -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@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. ___ 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] Chunks of missing WM
I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu mailto:whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] tksurfer - view only clusters from a certain nr of voxels
Hi Alex, you can't do that with tksurfer. You will have to run mri_surfcluster to create a new overlay with clusters smaller than 50 removed. doug ps. Please send emails to the FS list and not directly to me. thanks! On 12/14/2012 02:17 PM, Alex Hanganu wrote: Dear Douglas, I am using tksurfer for analysing the results. Can you pleasetell me - what flag should I use in order to limit the minimalthreshold of clusters to a certain number of voxels ? For example if I want to show only those significant clusters, which have at least 50 voxels. I couldn't find this answer in the wiki. Thanks !! Sincerely, Alex. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer - view only clusters from a certain nr of voxels
Thanks Douglas ! OK !! Alex. Le 14/12/2012 2:27 PM, Douglas N Greve a écrit : Hi Alex, you can't do that with tksurfer. You will have to run mri_surfcluster to create a new overlay with clusters smaller than 50 removed. doug ps. Please send emails to the FS list and not directly to me. thanks! On 12/14/2012 02:17 PM, Alex Hanganu wrote: Dear Douglas, I am using tksurfer for analysing the results. Can you please tell me - what flag should I use in order to limit the minimal threshold of clusters to a certain number of voxels ? For example if I want to show only those significant clusters, which have at least 50 voxels. I couldn't find this answer in the wiki. Thanks !! Sincerely, Alex. ___ 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] Interpretation of voxel values in TRACULA path.pd images
Hi Anastasia, Just follow up on this thread.. If 5000 samples were used for each voxel, how can I normalize the intensity of path.pd volumes to a sum of 1 ? Also what thresholding value was chosen to calculate the tract volume, shown in the pathstats.overall.txt ? Thanks. ping On Fri, Nov 9, 2012 at 10:56 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Jon - The path.pd volumes are indeed the posterior probability distributions of each pathway. They are not normalized to a sum of 1 though b/c they're estimated by a sampling algorithm (drawing sample paths from this unknown distribution and adding up the sample paths, instead of estimating the distribution directly). Hope this helps, a.y On Fri, 9 Nov 2012, Jon Clayden wrote: Dear all, I understand that the various path.pd image files that are created by TRACULA represent a posterior distribution over the corresponding tract location, but I was wondering if someone could explain to me exactly what the values in these images mean. I assume that they are not probabilities as such, since they have values ranging up to several hundreds. Thanks in advance, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] regarding use-mritotal
Hi, this link: http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 discusses a solution to bad talairach.xfm transforms, the -use-mritotal flag. this link: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV mentions that the talairach.xfm is used to calculate the total intracranial volume. is using mritotal likely to result in significantly different intracranial volumes even if the talairach.xfm does not appear to be very different when viewed? thanks much, -eric ___ 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] Contents of SUBJECTS_DIR
Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in * /media/Dell/_FS/buckner_data/* (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of * /home/virtualuser/freesurfer/subjects*. The tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Datasuggests that the data set should be inside *$FREESURFER_HOME/subjects*, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be*/media/Dell/_FS/buckner_data/ *, but then the first command of the analysis (mris_preproc) says it can't find fsaverage! The command only works if I create a new folder and copy the following in there: - the contents of */group_analysis_tutorial* (i.e. folders of the type * 004*, *008*, ..), and - the contents of* /home/virtualuser/freesurfer/subjects* (i.e. folders such as *bert*, *fsaverage*, ..) ..and then run the command from there -- however, this seems very cumbersome and takes a lot of time. My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default */subjects* folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary? Many thanks for any help! Tudor ___ 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] Contents of SUBJECTS_DIR
Hi Tudor, you can create a symbolic link to fsaverage rather than copying it. doug On 12/14/2012 04:18 PM, Tudor Popescu wrote: Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in //media/Dell/_FS/buckner_data// (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of //home/virtualuser/freesurfer/subjects/. The tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data suggests that the data set should be inside /$FREESURFER_HOME/subjects/, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be//media/Dell/_FS/buckner_data//, but then the first command of the analysis (mris_preproc) says it can't find fsaverage! The command only works if I create a new folder and copy the following in there: * the contents of //group_analysis_tutorial/ (i.e. folders of the type /004/, /008/, ..), and * the contents of//home/virtualuser/freesurfer/subjects/ (i.e. folders such as /bert/, /fsaverage/, ..) ..and then run the command from there -- however, this seems very cumbersome and takes a lot of time. My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default //subjects/ folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary? Many thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Chunks of missing WM
it doesn't, although the 5.2 mri_normalize should help as well cheers Bruce On Fri, 14 Dec 2012, Jonathan Holt wrote: OK this is great. Does this require the latest version of Freesurfer? I see recon-all v 5.2, we're running Freesurfer 5.0.0 for reference On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote: I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] Contents of SUBJECTS_DIR
On 12/14/2012 04:51 PM, Tudor Popescu wrote: Thanks Doug! I tried figuring out how to create symlinks manually (as I think recon-all has already been run in the case of the group analysis tutorial, therefore they were not generated automatically) but could not find anything helpful on the wiki. cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage I also looked for a tutorial on how to run recon-all on raw NIFTI files (which I guess first have to be converted to MGZ), as I'd first have to do this step to my own data before starting to follow the steps described in the group analysis tutorial. You can just spec the nifti file as input (--i file.nii), you do not need to convert doug Tudor On 14 December 2012 21:23, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Tudor, you can create a symbolic link to fsaverage rather than copying it. doug On 12/14/2012 04:18 PM, Tudor Popescu wrote: Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in //media/Dell/_FS/buckner_data// (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of //home/virtualuser/freesurfer/subjects/. The tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data suggests that the data set should be inside /$FREESURFER_HOME/subjects/, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be//media/Dell/_FS/buckner_data//, but then the first command of the analysis (mris_preproc) says it can't find fsaverage! The command only works if I create a new folder and copy the following in there: * the contents of //group_analysis_tutorial/ (i.e. folders of the type /004/, /008/, ..), and * the contents of//home/virtualuser/freesurfer/subjects/ (i.e. folders such as /bert/, /fsaverage/, ..) ..and then run the command from there -- however, this seems very cumbersome and takes a lot of time. My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default //subjects/ folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary? Many thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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
[Freesurfer] ooops deleted fsaverage
do I need to download the whole freesurfer package again to get it? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
