Re: [Freesurfer] pwd: permission denied
Hi Marcel: Do you using Mac? If so, please unlock your root account, then change to the root account (re-login as root or using 'su' command in terminal window). We also have this problem one month ago. It is because that the default setting for root account in OS X 10.7.x is hidden in the beginning, and FS need root account to operate. So if your OS X is upgraded to 10.7.x, then you will have problem. The FS ran smoothly under our old version OS X (10.6.x). Hope this help. 2012/3/6 Marcel Zwiers m.zwi...@fcdonders.ru.nl: Hi Michael, Thanks for your help and suggestions! I'd have to try to recreate the error, but I have an idea of what it could be (assuming /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1 is a directory). Actually not yet, /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness is a directory but BIG1026_1 is supposed to be created by recon-all (but wasn't as a consequence of the error). While you may have read, write, and execute permissions to your colleague's directory, you must make sure that these permissions have been recursively added to the contents of that directory (child directories, child directory files, and directory files). There are only *.nii.gz files in that directory plus a few extra files and (symbolic links to) folders that I assume should have nothing to do with the error? The content looks like this (ls -al): drwxrwxr-x 2 marhoo big 352256 Mar 6 09:51 ./ drwxrwx--x 15 marhoo big 4096 Feb 29 15:49 ../ -rw--- 1 marzwi big 12219623 Mar 2 16:06 BIG1026_1.nii.gz [..] -rw--- 1 marzwi big 12219623 Mar 2 16:06 BIG4025_1.nii.gz -rw-rwxr-- 1 marhoo big75806 Feb 27 10:54 BIG_aseg_stats.log* lrwxrwxrwx 1 marhoo big 34 Feb 19 09:12 fsaverage - /opt/freesurfer/subjects/fsaverage/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 lh.EC_average - /opt/freesurfer/subjects/lh.EC_average/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 rh.EC_average - /opt/freesurfer/subjects/rh.EC_average/ -rw-rwxr-- 1 marhoo big18200 Sep 27 10:39 v5.0.txt* -rw-rwxr-- 1 marhoo big 3220 Sep 27 10:39 v5.1.txt* -rw-rwxrw- 1 marhoo big 523 Feb 24 10:07 .xdebug_tkmedit* I believe that your problem is that the file BIG1026_1.nii.gz (however, from my experience this file should not simply be in the BIG1026_1 folder but in the orig directory of the mri folder) has not inherited the specified permissions from its parent directory. My username is marzwi, I am member of the big group and I have rw permissions of all the files and directories (see listing above). If this does not correct the error, set the environmental SUBJECTS_DIR variable to the directory housing the subject directories (making sure that your colleague gives you sufficient access to this directory), lose the -sd path in the command, and make sure that you have read, write, execute permissions recursively added to the directories and files that you will be working with. I did that but the error message remains. Here's the full message, started from a newly opened bash terminal: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer FSFAST_HOME /opt/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/subjects MNI_DIR /opt/freesurfer/mni FSL_DIR /opt/fsl mentat002:$ export SUBJECTS_DIR=/home/mrphys/marzwi/BIG/Freesurfer_CorticalThickness mentat002:$ recon-all -subject BIG1026_1 -i BIG1026_1.nii.gz -autorecon1 /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied cp: cannot create regular file `/BIG1026_1/scripts/build-stamp.txt': No such file or directory cat: /BIG1026_1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is Actual FREESURFER_HOME /opt/freesurfer-v5.1 /BIG1026_1: No such file or directory. Another option would be if your colleague set up a subjects directory within his parent directory and add each subject's folder to this directory and then setting this as your SUBJECTS_DIR variable (ensuring you have read, write, execute permissions). I created a subfolder, copied the BIG1026_1.nii.gz file into it and ran recon-all using this subfolder as SUBJECTS_DIR but I kept getting permission denied errors. I hope this helps; however, not knowing the version of free surfer that you are running nor the operating system makes it difficult to troubleshoot your problem. Let me know if you arrive at a solution or require further assistance. Thanks, Michael Nowak I hope the info above can help troubleshooting my problem. Thanks a lot Michael! Cheers,
[Freesurfer] About new FS version
Dear FS experts I've seeing that a new version of FS is about to be realized, but I'm wondering how soon will be it.Bests,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] How to find the anatomical slices in the data?
Dear All, Now I have some datas which are including anatomical data and function data,and I want to find the anatomical slices from them to run command 'recon-all'.How can I do? Yours ___ 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] save custom made path on surface as label
Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax:+49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-genc/ ___ 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] aparc.a2005s+aseg.mgz
Dear Freesurfer Mavens, After running recon-all -all on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data? Thanks for your help. Best, Mark Senior Research Scientist Division of Gastroenterology and Hepatology Departmernt of Medicine Medical College of Wisconsin Milwaukee, WI ___ 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] mri_label2vol cannot allocate memory
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to find the anatomical slices in the data?
if it's Siemens dicoms you can try unpacksdcmdir On Wed, 7 Mar 2012, bowan...@mail.ustc.edu.cn wrote: Dear All, Now I have some datas which are including anatomical data and function data,and I want to find the anatomical slices from them to run command 'recon-all'.How can I do? Yours ___ 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] qdec
Hi Julia, Please try deleting the space in 'Left Amygdala' and 'Right Amygdala' in your test.dat file and rerun qdec. Sita. On Wed, 7 Mar 2012, Richter, Julia wrote: Dear Sir or Madam, I have a question concerning FreeSurfer. At the moment I am trying to run a qdec analysis. I have already written the qdec.table.dat (attached, labeled test.dat) and a file labeled diagnosis.level.dat, in which all possible levels are listed (also attached). When I try to load the data table, I get an error message (as you can see in the attached screenshot). Can you please help me to solve the problem? Thanks a lot, yours sincerely, Julia Richter ___ 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] save custom made path on surface as label
Yes, you probably need to generate a closed path, or a closed cut. I'm not sure if we support saving paths as label files. Anyone know? Bruce On Wed, 7 Mar 2012, Erhan Genc wrote: Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-genc/ ___ 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] mri_label2vol cannot allocate memory
Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony ___ 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] White Matter question
Dear all, I was wondering if you have encountered this issue before: Would you anticipate a difference between the volume calculated by Freesurfer 5.0 in Cerebral-White-Matter volume and the total volume calculated from the regions (defined by the Desikan atlas) in wmparc.stats? In one of my studies, the Cerebral-White-Matter volume is bigger than the volume obtained by summing up the regions in wmparc.stats on average and for individual patients as well. Is there an anatomical reason behind this? Which measure should be preferentially used? Help would be much appreciated. Thanks, Dhinakaran. ___ 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] Interpreting Results
Hi Allie the real question is whether the surfaces are accurate in that place for that subject. The only way to tell is to visually inspect them. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce, I'm not sure if this qualifies as an outlier, but I do have one individual (and the age-matched control) who is much older than the rest (see attached). Do you think elimination of this subject could make the comparison possible? Thanks, Allie On Tue, Mar 6, 2012 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: do you have a big outlier in the thickness measures? I didn't see one. It seems unlikely that all your subject have a defect in that spot On Tue, 6 Mar 2012, Douglas N Greve wrote: It means that any comparison depends on age. Eg, if you compare them at an age where the lines cross, you will see no effect. If you compare them at age=0 (what you were doing before), then you see a big effect. Some statisticians will say that you cannot do the comparison in the presence of an interaction. dogu Allie Rosen wrote: So if my findings show that each group ages differently, does that mean I can't compare them at all because I can't regress out age? Or is there some way of comparing the groups despite this difference in aging patterns? Thanks again, Allie On Tue, Mar 6, 2012 at 4:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It might, don't know Allie Rosen wrote: Hi Doug, Yes, I think there actually may be a topologic defect in this area, although not directly where the cluster is (attached). Could this be the cause of the thickness result? If I go back and try to repair the defect, will that make the results more typical and, more importantly, correct? Thanks again, Allie On Tue, Mar 6, 2012 at 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Allie, yes, it means that each group is affected differently by age. The controls are increasing their thickness with age in this area (which seems strange, usually you expect general decreases with age). You might check the quality of the surfaces in this area. doug Allie Rosen wrote: Hi Doug, Thanks for the response. I've actually already run an interaction contrast and the same area is still significant (attached). I'm not sure how to interpret this either, unfortunately. Does it say that both groups are affected significantly differently by age? Can you tell me what it means? I'm having problems trying to do this myself. Thanks very much, Allie On Tue, Mar 6, 2012 at 3:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Allie, to be more precise, you have selected controlpatient regressing out the effects of age. This second part is the key. If you were to trace the regression lines back to age=0 (the meaning of regressing out age), then controlpatient by a wide margin. But you have a problem here in that the regression
Re: [Freesurfer] pwd: permission denied
Hallelujah ! Problem solved! Here's what happened: both tcsh pwd and /bin/pwd give errors when a directory is executable (+x) but not readable (-r). And in my case, the colleague of mine fully opened up $SUBJECTS_DIR for me, but (and this is also how it should be done) only provided me with executable rights for the parent directories. I haven't figured out why recon-all needs to call pwd on these parent directories at all -- I leave that one for the recon-all tcsh gurus :-) My hack was to replace every pwd call in the recon-all script by the built-in bash pwd call (which only needs +x permissions). It's not very pretty, but hey, must of us aren't! To be precise, this is what did it for me (NB: some of the pwd replacements may be unnecessary): diff myrecon-all /opt/freesurfer/bin/recon-all 296c296 set PWD = bash -c 'pwd'; --- set PWD = pwd; 298c298 # if ( -e /bin/pwd ) set PWD = /bin/pwd --- if ( -e /bin/pwd ) set PWD = /bin/pwd 361c361 set freesurfer_home_true = `$PWD`; --- set freesurfer_home_true = `pwd`; 382c382 $PWD $ENVF --- pwd $ENVF 3819c3819 echo PWD `$PWD` $ErrorFile --- echo PWD `pwd` $ErrorFile 3880c3880 set InVolDir = `$PWD`; --- set InVolDir = `pwd`; 4943c4943 setenv FREESURFER_HOME `$PWD`; --- setenv FREESURFER_HOME `pwd`; Hope this may be of use to anyone encountering the same problem and that this tcsh bin /bin/pwd problem may be taken into account in future recon-all versions. All the best and thanks a lot for all your time and kind help, Marcel. Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz -autorecon1 [..] However, if I run the same command on the same file, except that this file is now located in a directory of a colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects /BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 pwd: cannot open directory `../..': Permission denied /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied [..] From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause and hope you have any ideas here. Cheers, Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands___ 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] pwd: permission denied
Hallelujah ! Problem solved! Here's what happened: both tcsh pwd and /bin/pwd give errors when a directory is executable (+x) but not readable (-r). And in my case, the colleague of mine fully opened up $SUBJECTS_DIR for me, but (and this is also how it should be done) only provided me with executable rights for the parent directories. I haven't figured out why recon-all needs to call pwd on these parent directories at all -- I leave that one for the recon-all tcsh gurus :-) My hack was to replace every pwd call in the recon-all script by the built-in bash pwd call (which only needs +x permissions). It's not very pretty, but hey, must of us aren't! To be precise, this is what did it for me (NB: some of the pwd replacements may be unnecessary): diff myrecon-all /opt/freesurfer/bin/recon-all 296c296 set PWD = bash -c 'pwd'; --- set PWD = pwd; 298c298 # if ( -e /bin/pwd ) set PWD = /bin/pwd --- if ( -e /bin/pwd ) set PWD = /bin/pwd 361c361 set freesurfer_home_true = `$PWD`; --- set freesurfer_home_true = `pwd`; 382c382 $PWD $ENVF --- pwd $ENVF 3819c3819 echo PWD `$PWD` $ErrorFile --- echo PWD `pwd` $ErrorFile 3880c3880 set InVolDir = `$PWD`; --- set InVolDir = `pwd`; 4943c4943 setenv FREESURFER_HOME `$PWD`; --- setenv FREESURFER_HOME `pwd`; Hope this may be of use to anyone encountering the same problem and that this tcsh bin /bin/pwd problem may be taken into account in future recon-all versions. All the best and thanks a lot for all your time and kind help, Marcel. Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz -autorecon1 [..] However, if I run the same command on the same file, except that this file is now located in a directory of a colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects /BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 pwd: cannot open directory `../..': Permission denied /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied [..] From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause and hope you have any ideas here. Cheers, Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands___ 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] FS 5.1 control points problem
Hi Tanja, Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM. Sita. On Wed, 7 Mar 2012, Tetiana Dadakova wrote: Dear FS list, We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1). I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_label2vol cannot allocate memory
Hi Anthony, what's in chuman_1.mgz? How many labels? doug Anthony Dick wrote: Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB RAM. Anthony -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed squashed) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ 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] Interpreting Results
Hi Bruce and Doug, Given the fact that all my surfaces for my 16 patients and controls are fine, I'm still left with some basic questions: Since there is this interaction effect for age, how can I actually compare the thickness of the two populations? And should I be worried about the fact that some areas are thickening with age, despite the fact that this isn't caused by defects in the surface topology of the subjects? Thank you for the help, Allie On Wed, Mar 7, 2012 at 10:02 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Allie the real question is whether the surfaces are accurate in that place for that subject. The only way to tell is to visually inspect them. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce, I'm not sure if this qualifies as an outlier, but I do have one individual (and the age-matched control) who is much older than the rest (see attached). Do you think elimination of this subject could make the comparison possible? Thanks, Allie On Tue, Mar 6, 2012 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: do you have a big outlier in the thickness measures? I didn't see one. It seems unlikely that all your subject have a defect in that spot On Tue, 6 Mar 2012, Douglas N Greve wrote: It means that any comparison depends on age. Eg, if you compare them at an age where the lines cross, you will see no effect. If you compare them at age=0 (what you were doing before), then you see a big effect. Some statisticians will say that you cannot do the comparison in the presence of an interaction. dogu Allie Rosen wrote: So if my findings show that each group ages differently, does that mean I can't compare them at all because I can't regress out age? Or is there some way of comparing the groups despite this difference in aging patterns? Thanks again, Allie On Tue, Mar 6, 2012 at 4:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: It might, don't know Allie Rosen wrote: Hi Doug, Yes, I think there actually may be a topologic defect in this area, although not directly where the cluster is (attached). Could this be the cause of the thickness result? If I go back and try to repair the defect, will that make the results more typical and, more importantly, correct? Thanks again, Allie On Tue, Mar 6, 2012 at 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.**harvard.edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.**harvard.edugr...@nmr.mgh.harvard.edu wrote: Hi Allie, yes, it means that each group is affected differently by age. The controls are increasing their thickness with age in this area (which seems strange, usually you expect general decreases with age). You might check the quality of the surfaces in this area. doug Allie Rosen wrote: Hi Doug, Thanks for the response. I've actually already run an interaction contrast and the same area is still significant (attached). I'm not sure how to interpret this either, unfortunately. Does it say that both groups are affected significantly differently by age? Can you tell me what it means? I'm having problems trying to do this myself. Thanks very much, Allie On Tue, Mar 6, 2012 at 3:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.**harvard.edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.**harvard.edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.**harvard.edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
Re: [Freesurfer] Interpreting Results
Hi Allie perhaps David Salat (ccd) can comment. He definitely saw some areas that thickened with age. They weren't common, but they were definitely in the data. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce and Doug, Given the fact that all my surfaces for my 16 patients and controls are fine, I'm still left with some basic questions: Since there is this interaction effect for age, how can I actually compare the thickness of the two populations? And should I be worried about the fact that some areas are thickening with age, despite the fact that this isn't caused by defects in the surface topology of the subjects? Thank you for the help, Allie On Wed, Mar 7, 2012 at 10:02 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Allie the real question is whether the surfaces are accurate in that place for that subject. The only way to tell is to visually inspect them. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce, I'm not sure if this qualifies as an outlier, but I do have one individual (and the age-matched control) who is much older than the rest (see attached). Do you think elimination of this subject could make the comparison possible? Thanks, Allie On Tue, Mar 6, 2012 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: do you have a big outlier in the thickness measures? I didn't see one. It seems unlikely that all your subject have a defect in that spot On Tue, 6 Mar 2012, Douglas N Greve wrote: It means that any comparison depends on age. Eg, if you compare them at an age where the lines cross, you will see no effect. If you compare them at age=0 (what you were doing before), then you see a big effect. Some statisticians will say that you cannot do the comparison in the presence of an interaction. dogu Allie Rosen wrote: So if my findings show that each group ages differently, does that mean I can't compare them at all because I can't regress out age? Or is there some way of comparing the groups despite this difference in aging patterns? Thanks again, Allie On Tue, Mar 6, 2012 at 4:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It might, don't know Allie Rosen wrote: Hi Doug, Yes, I think there actually may be a topologic defect in this area, although not directly where the cluster is (attached). Could this be the cause of the thickness result? If I go back and try to repair the defect, will that make the results more typical and, more importantly, correct? Thanks again, Allie On Tue, Mar 6, 2012 at 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Allie, yes, it means that each group is affected differently by age. The controls are increasing their thickness with age in this area (which seems strange, usually you expect general decreases with age). You might check the quality of the surfaces in this area. doug Allie Rosen wrote: Hi Doug, Thanks for the response. I've actually already run an interaction contrast and the same area is still significant (attached). I'm not sure how to interpret this either, unfortunately. Does it say that both groups are affected significantly differently by age? Can you
[Freesurfer] FreeSurfer Course in Amsterdam!
Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.freesurfercourseamsterdam.nl/ Questions about the Amsterdam course should go to Veronica Popescu (i...@freesurfercourseamsterdam.nl). Hope to see you there, Allison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed squashed) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
are there other mni tools installed? are the variables from the different freesurfer installs getting mixed? n. On Wed, 2012-03-07 at 19:01 +, Ian Charest wrote: Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.html but in this user’s case there seemed to be a problem with the MPRAGE image itself (the brain seemed “squashed”) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ 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] Fwd: Qdec Error in analyze: command failed
Hi All, Just wanted to follow up on my message below. Thank you! Laura. -- Forwarded message -- From: Laura Tully tully.la...@googlemail.com Date: Mon, Mar 5, 2012 at 2:03 PM Subject: Qdec Error in analyze: command failed To: freesurfer@nmr.mgh.harvard.edu Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table loading completed successfully. SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? Nuisance factors: ICV_Mean_Centered 1.000 0.000 0.000; lh-Avg-thickness-Social_Fx-Cor --- Does the correlation between thickness and Social_Fx differ from zero? Nuisance factors: ICV_Mean_Centered 0.000 1.000 0.000; sh: ICV/y.mgh: No such file or directory ninputs = 29 Checking inputs nframestot = 29 Allocing output Done allocing nframes = 29 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx unknown file type for file (/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx) Error in Analyze: command failed: mri_concat /ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh --o /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFxICV/y.mgh -- Laura Tully Social Neuroscience Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu -- Laura Tully Social Neuroscience Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi Ian, This is a bug in the CBU's freesurfer wrappers written at the CBU site and not a FreeSurfer bug. Ask them to look into fixing it. Basically, the wrapper doesn't transfer all the variables necessary for FreeSurfer to run properly. The only work around for you at the moment would be to run it locally i.e. not use the CBU's wrappers. D Nick Schmansky wrote: are there other mni tools installed? are the variables from the different freesurfer installs getting mixed? n. On Wed, 2012-03-07 at 19:01 +, Ian Charest wrote: Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.html but in this user’s case there seemed to be a problem with the MPRAGE image itself (the brain seemed “squashed”) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ 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
[Freesurfer] Cluster-Size in Qdec
Dear Freesurfer experts, I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan ___ 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] recon2 error
Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-all) and I keep getting this error message when it gets to recon2 : pass 1 of 1 setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... : dt=0.000, rms=0.789, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26136.459 ms 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24108.512 ms and it continues this way on and on. I tried to run recon-all again on an old subject (on which it worked this summer) by renaming the files and folders of course and I got the same error message. I uninstalled and reinstalled FreeSurfer and still am getting the message. I ran one of the subject on my colleagues machine (which is slower than mine; took him 22 hours) and it worked perfectly. Can anyone tell me what could be the problem ? I will need to run more analyses in a few months and I need to fix it ASAP. Here's the command I'm using (which is the same as my colleague and as indicated on FS wiki) : recon-all -subjid a_al_t1 -i ~/Documents/T1W_3D_TFE/GHA_A-C_2234495-T1W_3D_TFE-20101207-301-1.dicom -all Thank you, Jimmy ___ 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] recon2 error
Hi Jimmy that isn't an error message - just an informational one. How long did you wait? Are you sure it is not going to terminate if you let it run long enough? cheers Bruce On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-all) and I keep getting this error message when it gets to recon2 : pass 1 of 1 setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... : dt=0.000, rms=0.789, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26136.459 ms 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24108.512 ms and it continues this way on and on. I tried to run recon-all again on an old subject (on which it worked this summer) by renaming the files and folders of course and I got the same error message. I uninstalled and reinstalled FreeSurfer and still am getting the message. I ran one of the subject on my colleagues machine (which is slower than mine; took him 22 hours) and it worked perfectly. Can anyone tell me what could be the problem ? I will need to run more analyses in a few months and I need to fix it ASAP. Here's the command I'm using (which is the same as my colleague and as indicated on FS wiki) : recon-all -subjid a_al_t1 -i ~/Documents/T1W_3D_TFE/GHA_A-C_2234495-T1W_3D_TFE-20101207-301-1.dicom -all Thank you, Jimmy ___ 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] recon2 error
I waited a whole night ... I don't recall getting this message last summer. I will run it again and check it back again on Friday just to be sure. Thank you, Jimmy On Wed, Mar 7, 2012 at 15:44, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jimmy that isn't an error message - just an informational one. How long did you wait? Are you sure it is not going to terminate if you let it run long enough? cheers Bruce On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-all) and I keep getting this error message when it gets to recon2 : pass 1 of 1 setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... : dt=0.000, rms=0.789, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26136.459 ms 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24108.512 ms and it continues this way on and on. I tried to run recon-all again on an old subject (on which it worked this summer) by renaming the files and folders of course and I got the same error message. I uninstalled and reinstalled FreeSurfer and still am getting the message. I ran one of the subject on my colleagues machine (which is slower than mine; took him 22 hours) and it worked perfectly. Can anyone tell me what could be the problem ? I will need to run more analyses in a few months and I need to fix it ASAP. Here's the command I'm using (which is the same as my colleague and as indicated on FS wiki) : recon-all -subjid a_al_t1 -i ~/Documents/T1W_3D_TFE/GHA_A-** C_2234495-T1W_3D_TFE-20101207-**301-1.dicom -all Thank you, Jimmy The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon2 error
a whole night may not be enough depending on the speed of your machine, and how far from our atlas anatomy your subject is. Those messages are normal and part of the most computationally intensive step in recon-all, so see if it take a day or so to finish On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: I waited a whole night ... I don't recall getting this message last summer.I will run it again and check it back again on Friday just to be sure. Thank you, Jimmy On Wed, Mar 7, 2012 at 15:44, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jimmy that isn't an error message - just an informational one. How long did you wait? Are you sure it is not going to terminate if you let it run long enough? cheers Bruce On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-all) and I keep getting this error message when it gets to recon2 : pass 1 of 1 setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... : dt=0.000, rms=0.789, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26136.459 ms 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24108.512 ms and it continues this way on and on. I tried to run recon-all again on an old subject (on which it worked this summer) by renaming the files and folders of course and I got the same error message. I uninstalled and reinstalled FreeSurfer and still am getting the message. I ran one of the subject on my colleagues machine (which is slower than mine; took him 22 hours) and it worked perfectly. Can anyone tell me what could be the problem ? I will need to run more analyses in a few months and I need to fix it ASAP. Here's the command I'm using (which is the same as my colleague and as indicated on FS wiki) : recon-all -subjid a_al_t1 -i ~/Documents/T1W_3D_TFE/GHA_A-C_2234495-T1W_3D_TFE-20101207-301-1.dicom -all Thank you, Jimmy 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] Cluster-Size in Qdec
I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size. With a few tricks you can remove the ones over a certain size too. doug Dusan Hirjak wrote: Dear Freesurfer experts, I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] White Matter question
yes, the cerebral white matter is surface-based, so it can take into account sub-voxel resolution of the surfaces. The WMParc is just counting voxels. Dhinakaran Chinappen wrote: Dear all, I was wondering if you have encountered this issue before: Would you anticipate a difference between the volume calculated by Freesurfer 5.0 in Cerebral-White-Matter volume and the total volume calculated from the regions (defined by the Desikan atlas) in wmparc.stats? In one of my studies, the Cerebral-White-Matter volume is bigger than the volume obtained by summing up the regions in wmparc.stats on average and for individual patients as well. Is there an anatomical reason behind this? Which measure should be preferentially used? Help would be much appreciated. Thanks, Dhinakaran. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Smart concatenation in selxavg3-sess?
Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses smart concatenation to combine each run's data -- what is smart concatenation? How does are the runs brought into alignment? Thanks! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT ___ 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] aparc.a2005s+aseg.mgz
Hi Mark, was aparc.a2009s+aseg.mgz created? That is the new one. doug On 3/7/12 8:43 AM, Kern, Mark wrote: Dear Freesurfer Mavens, After running recon-all -all on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data? Thanks for your help. Best, Mark Senior Research Scientist Division of Gastroenterology and Hepatology Departmernt of Medicine Medical College of Wisconsin Milwaukee, WI ___ 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] Smart concatenation in selxavg3-sess?
The runs are brought into alignment during preprocessing. The default is to motion correct each run to the middle time point of the run, then sample the entire run to the common spaces (left hemi fsaverage, right hemi, or the MNI305 for subcortical volume). Once this is done, all the runs are in alignment. The data are simply concatenated together. The smart part comes when constructing the design matrix. To account for different drifts and offsets in each run, separate nuisance terms are provided for each run in the design matrix. There is really nothing fancy here. A number of years ago, people would just concatenate all their runs and then analyze it as if it came from one run. This is not a good idea, and the word concatenation got a bad reputation. I used the term smart concatenation to distinguish between the two methods and to prevent any knee-jerk reaction from simply saying that we're concatenating the runs together. doug On 3/7/12 7:56 PM, Alex Kell wrote: Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses smart concatenation to combine each run's data -- what is smart concatenation? How does are the runs brought into alignment? Thanks! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT ___ 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.
