[Freesurfer] Dimension of brain
Dear FS experts, I'd like to know the fsaverage brain (rendered brain) generated after recon-all analysis is same as that of individuals brain size. I mean is rendered brain developed after recon-all = individual brain?? If not, How much cm/mm away or towards the original brain?? ___ 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] License problem
Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands: csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/nru/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- W have another server still running the older OpenSuse version and there it works without any problems. There hasn't been done any changes to the freesurfer installation directory and it is the same shared NFS mounted directory at both servers. Please help us finding out how to correct this problem so we can use Freesurfer again. Thanks for the help Claus Svarer attachment: Claus_Svarer.vcf___ 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] Editing masks
Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua ___ 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 resolution
Hi Joerg I think Jon Polimeni (ccd) might have some tools for this, but it's not something we routinely do cheers Bruce On Tue, 11 Jun 2013, Jörg Pfannmöller wrote: Hello FSexperts, I am investigating a small area on the cortex. If this area is diplayed by tksurfer the lable outlines and the transition in the colors indicating the curvature looks rather low resolved. Probably this just shows the resolution of the fsaverage brain lattice. Is there a way to improve this and to make it look more smooth without smoothing the data? With other words, is it possible to artificially increase the resolution? Regards Joerg ___ 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] Dimension of brain
Hi Anupa sorry, I don't understand the question. Fsaverage is the average of a bunch of subjects (40 or so I think). What do you mean by size? It certainly has less surface area than any individual in it, since the averaging smnooths it. We store this in the surface so that we can correct for it e.g. when doing surface-based smoothing Bruce On Mon, 10 Jun 2013, Anupa AV wrote: Dear FS experts, I'd like to know the fsaverage brain (rendered brain) generated after recon-all analysis is same as that of individuals brain size. I mean is rendered brain developed after recon-all = individual brain?? If not, How much cm/mm away or towards the original brain?? ___ 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] Editing masks
Hi Joshua are you using the surfaces for this? If so, you shouldn't as they are undefined in those regions (since they have internal laminar structure that is different than what we expect). What are you trying to achieve? cheers Bruce On Tue, 11 Jun 2013, Joshua deSouza wrote: Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua ___ 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] Parameterization Optseq
Dear Doug, Thanks you for your e-mail and sorry for the inconvenience. Here is the code again. In this line of code we included the fixed duartion of the fix (1.0) in the event duration specification (summing to 5.0) and asked Optseq to insert null events of a minimum duration of 0.0 in 25% of the total scanning time: --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 5.0 8.0 --ev Gain4 5.0 8.0 --ev Gain6 5.0 8.0 --ev Gain8 5.0 8.0 --ev Loss2 5.0 8.0 --ev Loss4 5.0 8.0 --ev Loss6 5.0 8.0 --ev Loss8 5.0 8.0 --ev Catch 5.0 8.0 --tnullmin 0.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test2 In this line of code we did not include the fixed duration of the fix (1.0) in the event duration specification, but instead asked Opseq to insert null events of at minimum 1.0 sec: --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test3 Since the former code yielded an error, we cut down the number of time points, in the following code. This worked, but no longer yielded extra null events in 25% of the scan time, because scan down was less now. --ntp 180 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test4 I hope this is helpful in understanding our problem and helping us out. Thank you for your time! Best, Laura 2013/6/7 Douglas N Greve gr...@nmr.mgh.harvard.edu Hi Laura, can you just cut and paste the command line into the email? There are some funny characters in that file you sent doug On 06/07/2013 12:09 PM, Laura Dekkers wrote: Dear Doug, Thank you for your e-mail. Please find attached our command line. We felt that the first two lines of code should essentially yield the same timing of events. In the first we included the fixed duration of the fix (1.0) in our event duration (4.0) and meant to ask for extra null events of a minimum duration of 0.0 sec. In the second, we did not include the fixed duration of the fix in our event duration (4.0) and meant to ask for this by inserting null events of at least 1.0 sec. Since the second line of code yielded an error, we run the third line. Is this helpful? Best, Laura 2013/6/5 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Laura, what is your command line? doug On 06/04/2013 09:02 AM, Laura Dekkers wrote: Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out? Our task consists of 3 runs of 72 trails each, in which participants are presented with a fixation cross that remains on the screen for a fixed duration of 1 sec, followed by one out of nine different stimuli that remains on the screen for a fixed duration of 4 sec. This gives a scan duration of 360 sec. We would then like to add 25% jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this results in 225 time points. However, Optseq yields an error if ntp is set to 225, ev duration set to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 ERROR: could not enforce tNullMax=6 (ntries=10) You will need to reduce the number of time points or increase the number of presentations. However, reducing the number of time points makes Optseq to only insert null events of 1.0 or rarely 2.0 sec without much variation. Optimization with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and tnullmax to 6.0 does work. However, this renders Optseq to insert null events of a fixed duration op 1.0 sec, which is not what we want. Could you please advise us in how to set these parameters? Thank you in advance. Best regards, Laura Dekkers -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental
[Freesurfer] Problem after installation of the newest security updates for MacOSX
Dear FS experts After the installation of the newest Mac OS X security updates, the following error occurred: [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% tksurfer bert lh pial dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /usr/X11/lib/libGL.1.dylib Reason: Incompatible library version: libGL.1.dylib requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Trace/BPT trap [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% Any idea to fix it easily is highly appreciated. Cheers Jürgen Hänggi Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] vertices don't match
Hi Doug, I have the v5.3 and the same problem in -qcache step (number of vertices do not match surface). I tried some suggestions such as recon-all -s subjid -vno-check; recon-all ..-make all; recon-all -s -surfvolume and I have the same results: Error: number of vertices do not match surface. However, if I do the mris_preproc mri_surf2surf with uncached data, I do not obtain the error and I can perform well the mri_glmfit. Is there any other option I can try to perform the analysis using the -qcache command?? Thanks in advance 2012/9/22 Douglas N Greve gr...@nmr.mgh.harvard.edu Try running recon-all -surfvolume ... doug On 09/20/2012 02:03 PM, Darren Gitelman wrote: Dear List I am adding to the post on this error from yesterday regarding problems with running qcache. I know this has been posted to the list before, but the suggested fixes and checks don't fix the problem. See the error below (ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file) 1) Running recon-all -s subjid -vno-check does not find any problems. It says everything is verified and checks out ok. 2) Running recon-all -s subjid -make all returns the message: make: Nothing to be done for `all'. But when I try recon-all -s subjid -qcache I get the error on this and several other subjects, but not all subjects. Checking the modification times on some files it looks like the thickness file came after the curv file. [drg@quser03 surf]$ ll *.thickness -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness [drg@quser03 surf]$ ll *.curv -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv Any suggestions for fixing the qcache error would be appreciated. Darren -- --- #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -- --- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6938/3300.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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. -- /**\ Francisco Javier Navas Sánchez Laboratorio de Imagen Médica U.M.C.E. Hospital General Universitario Gregorio Marañón Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jna...@hggm.es http://image.hggm.es
[Freesurfer] Faculty Members and Postdoctoral Fellows in Brainnetome
Dear all, *Faculty Members and Postdoctoral Fellows in Brainnetome* * * Please find the details below: http://www.brainnetome.org/en/job PS. If you also go to attend the OHBM 2013 in Seattle, you can find us at booth 218 at the exhibitor region. Date a meeting time by email to brainnet...@gmail.com would be appreciated. *Faculty Members and Postdoctoral Fellows in Brainnetome* Brainnetome Center (www.brainnetome.org) and National Laboratory of Pattern Recognition, Institute of Automation of Chinese Academy of Sciences (CASIA), seeks several postdoctoral fellows and faculty members from assistant to full professor levels in neuroimaging and brainnetome. We specifically seek individuals with expertise in one of the following fields: magnetic resonance imaging, especially diffusion MRI and functional MRI, optical imaging, medical image processing and analysis, pattern recognition. Brainnetome Center at CASIA has established its international reputation in neuroimaging, brain networks, and their applications in brain diseases. It also has established strong collaboration networks with a number of prestigious national and international laboratories and hospitals through Brainnetome consortium (www.brainnetome.org ). The faculty members have chance to work in an Australian partner laboratory on Neuroimaging and Brainnetome at Queensland Brain Institute (www.qbi.uq.edu.au ). * * *Minimum Qualifications:* The position requires a Ph.D. degree in brain imaging, neuroscience, cognitive neuroscience, neuroanatomy, psychiatry and neurology or a related field. Experience in* brain imaging such as MRI/EEG/MEG/fNIRS*, fluent verbal and written communication skills in English are also required, for the candidates with PhD in engineering, strong computer programming skills in Matlab and/or C++ language is a must. *Preferred Qualifications:* Good experience and background knowledge in the research focus areas: brain imaging. [image: *] Ability to work independently and in a team. [image: *] Capability to design and perform experimental plans; knowledge with sensor systems; strong interest to learn, understand statistical analysis procedures and interpret data. [image: *] Sufficient interpersonal skills in dealing with students (graduate and undergraduate), university personnel and other related groups. [image: *] Self-motivation and creativity are highly desirable. *Application Materials:* Applicants should send an e-mail attachment of a cover letter with a brief summary of *research background*, *curriculum vita *, *statement of research goals*, and *contact information of at least three referees* to brainnet...@gmail.com. Best wishes. Liu Yong Brainnetome Center National Laboratory of Pattern Recognition (NLPR) Institute of Automation, Chinese Academy of Sciences (CASIA) www.brainnetome.org/yongliu ___ 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] Environment variable HOME_FREESURFER
Dear Freesurfer experts, I am trying to install free surfer. It seems that my downloaded version does not have a .cshrc file. I only have an .sh and .csh file. All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file give me command not found. Any suggestion would be highly appreciated. Pablo ___ 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 measure the surface dimension in a mask image after mri_glmfit?
thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 measure the surface dimension in a mask image after mri_glmfit?
what is your full command line? On 6/11/13 10:04 AM, Glen Lee wrote: thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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. ___ 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] License problem
Hi Claus, I have never seen this before. Maybe Zeke has an idea? doug On 6/11/13 5:02 AM, Claus Svarer wrote: Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands: csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/nru/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- W have another server still running the older OpenSuse version and there it works without any problems. There hasn't been done any changes to the freesurfer installation directory and it is the same shared NFS mounted directory at both servers. Please help us finding out how to correct this problem so we can use Freesurfer again. Thanks for the help Claus Svarer ___ 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] Hippocampal subfields intensity
Hi, Eugenio,
TY again for your help. I did the computing without errors after your
suggestions. I also computed the intensities based on nu.mgz, norm.mgz
and T1.mgz. I would like to know the best measure I should consider,
including because I intend to compare these values with intensity data
from basal ganglia and cortical areas as I can find in aseg.stats. It
follows my results:
norm.mgz based
meannorm= 78.725
variancenorm = 20.258(stdev = 4.50001)
nu.mgz based
meannu = 87.362
variancenu = 26.343 (stdev =5.132543229)
T1.mgz based
meant1 = 84.023
variancet1 = 23.277 (stdev =4.824624338)
It follows the MatLab/Octave code I used
Norm=MRIread('norm_postres.mgz');
datanorm=Norm.vol(:);
Ps=nMRIread('posterior_right_subiculum.mgz');
postsub=double(Ps.vol(:));
meannorm=sum(datanorm.*postsub)/sum(postsub);
variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
Nu=MRIread('nu_postres.mgz');
datanu=Nu.vol(:);
meannu=sum(datanu.*postsub)/sum(postsub);
variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
T1=MRIread('T1_postres.mgz');
datat1=T1.vol(:);
meant1=sum(datat1.*postsub)/sum(postsub);
variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
The *postres.mgz files are nu, norm and T1 resampled as you suggested.
And nMRIread is the workarounded version of MRIread I said in previous
message.
Cheers,
Marcos
Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
(reslice like):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio
On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio
TY for your fast help. I understood you were suggesting to compute
that on MatLab and I tried this:
NU=MRIread('nu.mgz')### that runs ok
Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the
following message
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
I solved creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
With those changes I assigned 0 to mr-parms elements so it runs
without errors
But whe I tried the following line I copy and pasted from your
message:
mean=sum(Ps.*NU)/sum(Ps); ### I got the following error
Undefined function 'times' for input arguments of type 'struct'.
Any help?
Cheers, Marcos
PS: I promised I will post the final solution to list. But I guess it
is more didactic if these little problems are solved before.
TY, again.
Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio
On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.
105.59.
How could I get similar results for each hippocampal subfield,
assuming I also generated all posterior*.mgz files corresponding to
each subfield?
I guess I should first binarize each of the subfields file with a
threshold=127 to map all the pertinent voxels, and then use these
files as masks over nu.mgz and calculate the intensities values. But I
do not know the best way to accomplish this after the binarize step.
Thank you in advance for any help.
Marcos
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Re: [Freesurfer] License problem
Hi Doug After having sent the message to the mailing list this morning I found another mail sent to the mailing list a month ago about same problem: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28264.html I have tried to follow the thread but can't see that a solution was described. I therefor tried to email Nicola Toschi directly, but he has not answered yet. Let us see if he has found a solution for the problem. Kind regards Claus On 11-06-2013 16:46, Douglas Greve wrote: Hi Claus, I have never seen this before. Maybe Zeke has an idea? doug On 6/11/13 5:02 AM, Claus Svarer wrote: Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands: csvarer@hevesy:/usr/local/nru/freesurfer tkmedit -help -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/nru/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- W have another server still running the older OpenSuse version and there it works without any problems. There hasn't been done any changes to the freesurfer installation directory and it is the same shared NFS mounted directory at both servers. Please help us finding out how to correct this problem so we can use Freesurfer again. Thanks for the help Claus Svarer ___ 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. attachment: Claus_Svarer.vcf___ 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] autorecon3 error
I'm re-sending an old problem, because I received no answer. Cheers, Gabriel - Mensaje original - De: Gabriel Gonzalez Escamilla ggon...@upo.es Fecha: Lunes, 10 de Junio de 2013, 4:56 pm Asunto: Re: [Freesurfer] autorecon3 error A: Bruce Fischl fis...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Dear Doug Sorry for late answer. I did open as: tksurfer qsm1_17 lh inflated, and then File load surface lh.sphere.reg and tksurfer qsm1_17 lh sphere.reg Neither of them look bad, it looks very spherical, an has nothing strange to my eyes... Any other ideas??? Best Regards Gabriel - Mensaje original - De: Bruce Fischl fis...@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggon...@upo.es CC: freesurfer@nmr.mgh.harvard.edu Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ 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. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font ___ 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] autorecon3 error
Hi Gabriel something is wrong with some surface in the lh. Maybe your disk was full? Can you go through each of them and visualize them in tksurfer? One should fail (lh.orig, lh.white, lh.smoothwm, lh.inflated. lh.sphere, lh.sphere.reg) sorry I can't be more specific. I've never seen this particular error before Bruce On Tue, 11 Jun 2013, Gabriel Gonzalez Escamilla wrote: I'm re-sending an old problem, because I received no answer. Cheers, Gabriel - Mensaje original - De: Gabriel Gonzalez Escamilla ggon...@upo.es Fecha: Lunes, 10 de Junio de 2013, 4:56 pm Asunto: Re: [Freesurfer] autorecon3 error A: Bruce Fischl fis...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Dear Doug Sorry for late answer. I did open as: tksurfer qsm1_17 lh inflated, and then File load surface lh.sphere.reg and tksurfer qsm1_17 lh sphere.reg Neither of them look bad, it looks very spherical, an has nothing strange to my eyes... Any other ideas??? Best Regards Gabriel - Mensaje original - De: Bruce Fischl fis...@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggon...@upo.es CC: freesurfer@nmr.mgh.harvard.edu Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner4 0.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_ killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ 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. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font ___ 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
[Freesurfer] importing my data
Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C. ___ 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] importing my data
Clelia, Ide be willing to bet the error has something to do with the % sign in the path to the data file. Would it be possible for you to place the file somewhere such the the absolute path does not contain a % sign? -Zeke On 06/11/2013 12:37 PM, clelia pellicano wrote: Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C. ___ 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] importing my data
Hi clelia can you ls that file and confirm that exists? And check the permissions? Also, note that even if it had found it you didn't tell it to do anything. You probably want to specify -all on the recon-all command line as well. cheers Bruce On Tue, 11 Jun 2013, clelia pellicano wrote: Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C. ___ 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] importing my data
Hi, thank you so much, now it's working! I have deleted the % from the path (moving the files), and now it's ok. Thank you again, C. On Tue, Jun 11, 2013 at 5:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi clelia can you ls that file and confirm that exists? And check the permissions? Also, note that even if it had found it you didn't tell it to do anything. You probably want to specify -all on the recon-all command line as well. cheers Bruce On Tue, 11 Jun 2013, clelia pellicano wrote: Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%**201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%** 201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C. 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] importing my data
thanks Zeke! Bruce On Tue, 11 Jun 2013, clelia pellicano wrote: Hi, thank you so much, now it's working! I have deleted the % from the path (moving the files), and now it's ok. Thank you again, C. On Tue, Jun 11, 2013 at 5:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi clelia can you ls that file and confirm that exists? And check the permissions? Also, note that even if it had found it you didn't tell it to do anything. You probably want to specify -all on the recon-all command line as well. cheers Bruce On Tue, 11 Jun 2013, clelia pellicano wrote: Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C. 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] Fwd: Talairach Positioning in Horizontal View
Hi Peter, what scanner are you using? You might be better off with using a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that cleans it up. You can run just the talairaching with recon-all -s subject -schwartzya3t-atlas -talairach doug On 06/11/2013 01:03 PM, Peter Boulos wrote: I am very new to the software and have just begun assessing Talairach outputs for my subjects. I am confused in that I cannot seem to find a balance I am happy with between positioning of the green lines in both the horizontal and sagittal views for multiple subjects. I opened the talairach output with the following command (tkregister2 --mgz --s SUBJID --fstal --surf orig) and everything looked perfectly aligned for all the subjects I have tried in both the coronal and sagittal views but in the horizontal view the green lines went well off the back of the brain. I have attached a screenshot. I tried to translate the brain but that did not seem to solve my issue and I realized I needed to scale the length of the brain. When I did that I was more pleased with the outcome but the corpus callosum did not match up nearly as well after I did that (second attached screenshot) and that was the primary landmark I was using to pass my images in terms of talairach output assessment. Do you have any advice for me? Peter ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] License problem
Regarding any license issue under Opensuse 12.3 and the libcrypt incompatibility. So grab a libcrypt from an older opensuse (one where freesurfer was working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then add the location to the LD_LIBRARY_PATH environment variable so that freesurfer finds the old libcrypt. There is another workaround but you must contact Nick Schmansky, I don't remember the details. Thanks Nick ___ 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] Mean Regional Thickness
Has anyone published the mean cortical thickness of healthy older adults for all the Freesurfer ROI? I've only been able to find papers that report a of subset of the ROIs. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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] License problem
Thank you Nick for informing the list of this workaround. -Zeke On 06/11/2013 01:48 PM, Nick Jones wrote: Regarding any license issue under Opensuse 12.3 and the libcrypt incompatibility. So grab a libcrypt from an older opensuse (one where freesurfer was working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then add the location to the LD_LIBRARY_PATH environment variable so that freesurfer finds the old libcrypt. There is another workaround but you must contact Nick Schmansky, I don't remember the details. Thanks Nick ___ 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] Mean Regional Thickness
David might know Bruce On Tue, 11 Jun 2013, MCLAREN, Donald wrote: Has anyone published the mean cortical thickness of healthy older adults for all the Freesurfer ROI? I've only been able to find papers that report a of subset of the ROIs. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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] environment variable FREESURFER_HOME
Pablo, Attached are the original SetUpFreeSurfer.csh and SetUpFreeSurfer.sh files that come with the Freesurfer5.3 installation package. -Zeke On 06/11/2013 02:56 PM, pablo najt wrote: Thank you for your answer. There is another issue I am needing help with. As I have edited the .csh file from FreeSurfer I am not able to make it work any more. Is there a way to have a copy of the SetUpFreeSurfer.csh? I have downloaded the last version of Freesurfer for OSX 10.6.8 Thank you so much, Pablo Date: Tue, 11 Jun 2013 11:02:26 -0400 From: zkauf...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] environment variable FREESURFER_HOME Pablo, The .cshrc and .bashrc files we are referring to are not Freesurfer files and do not come with the Freesurfer distribution. They are files that can (although not always) exist in the home directory of your computer. Do not modify the the .csh or .sh files that come with Freesurfer. That is for the expert user. If you want to use Freesurfer just open a command line and type the following: (if using csh) setenv FREESURFER_HOME Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh (if using bash) export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If you dont want to type these commands everytime you want to start using freesurfer than you can add these lines to your .csh and .bashrc *in your home directory*. If those files do not exist than you may create them *in your home directory* and simply add those two lines to the file. -Zeke Dear Freesurfer experts, I am trying to install free surfer. It seems that my downloaded version does not have a .cshrc file. I only have an .sh and .csh file. All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file give me command not found. Any suggestion would be highly appreciated. Pablo Thank you for your response. It seems that my downloaded version does not have a .cshrc file. I only have an .sh and a .csh. What would you recommend to do? Should I reinstall FreeSurfer? Thanks. Pablo Date: Fri, 7 Jun 2013 18:16:56 -0400 From: zkauf...@nmr.mgh.harvard.edu To: pablon...@hotmail.com Subject: Re: [Freesurfer] environment variable FREESURFER_HOME There should be a file called .cshrc in your home directory. Add the two lines to that file. -Zeke On 06/07/2013 05:53 PM, pablo najt wrote: Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer:*/Applications/freesurfer* * * I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh But I am not sure where exactly I should add these lines. Do I need to edit the .csh file in Freesurfer. How should I do this? using Text Edit from apple would work? Thanks, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer SetUpFreeSurfer.csh Description: C-Shell script SetUpFreeSurfer.sh Description: application/shellscript ___ 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 does freesurfer take the individual landmarks of different regions take into acccount
Dear Bruce et al., Submitting a paper in which I use freesurfer for the analysis of the auditory cortex, I was asked how freesurfer actually takes individual boundaries (e.g. of Heschl's gyrus) into account? Both atlases (Desikan and Destrieux) are based on about 10-20 subjects. How are these boundaries transferred to other subjects? As far as I understood the description of freesurfer there aren't any templates (or some kind of masks) which are put on the subjects to analyse. What's the secret or principle behind the individual analysis to receive reliable data for every ROI of every subject (in a nutshell)? Thanks in advance, best wishes, Holger ___ 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 measure the surface dimension in a mask image after mri_glmfit?
Hi Doug -- I copied and pasted the summary file below. It looks like mask.mgh was treated as volumetric image. Also I'm not sure how to interpret TableCol. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ # cmdline mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat # sysname Linux # hostname rage.uphs.upenn.edu # machine x86_64 # user gel # anatomy_type volume # # SegVolFile mask.mgh # SegVolFileTimeStamp 2013/06/05 14:50:24 # InVolFile /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area # InVolFileTimeStamp 2013/05/22 16:49:43 # InVolFrame 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 1 # NTableCols 9 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8183781837.0 Seg0001 0.3836 0. 0.1297 1.1861 1.0563 On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Did you look in the summary file? If you have questions about that, can you send it? doug On 06/11/2013 11:34 AM, Glen Lee wrote: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: what is your full command line? On 6/11/13 10:04 AM, Glen Lee wrote: thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 tel:1%20%C2%A0%2081837%20%C2%**A081837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/**surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Hippocampal subfields intensity
Dear Marcos,
these are just mean and standard deviations of intensities of the images
at different levels of processing. What the best measure is depends on
what you want to do with them.
Cheers,
/Eugenio
On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio,
TY again for your help. I did the computing without errors after your
suggestions. I also computed the intensities based on nu.mgz, norm.mgz
and T1.mgz. I would like to know the best measure I should consider,
including because I intend to compare these values with intensity data
from basal ganglia and cortical areas as I can find in aseg.stats. It
follows my results:
norm.mgz based
meannorm= 78.725
variancenorm = 20.258(stdev = 4.50001)
nu.mgz based
meannu = 87.362
variancenu = 26.343 (stdev =5.132543229)
T1.mgz based
meant1 = 84.023
variancet1 = 23.277 (stdev =4.824624338)
It follows the MatLab/Octave code I used
Norm=MRIread('norm_postres.mgz');
datanorm=Norm.vol(:);
Ps=nMRIread('posterior_right_subiculum.mgz');
postsub=double(Ps.vol(:));
meannorm=sum(datanorm.*postsub)/sum(postsub);
variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
Nu=MRIread('nu_postres.mgz');
datanu=Nu.vol(:);
meannu=sum(datanu.*postsub)/sum(postsub);
variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
T1=MRIread('T1_postres.mgz');
datat1=T1.vol(:);
meant1=sum(datat1.*postsub)/sum(postsub);
variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
The *postres.mgz files are nu, norm and T1 resampled as you suggested.
And nMRIread is the workarounded version of MRIread I said in previous
message.
Cheers,
Marcos
Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
(reslice like):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio
On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio
TY for your fast help. I understood you were suggesting to compute
that on MatLab and I tried this:
NU=MRIread('nu.mgz')### that runs ok
Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the
following message
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
I solved creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
With those changes I assigned 0 to mr-parms elements so it runs
without errors
But whe I tried the following line I copy and pasted from your
message:
mean=sum(Ps.*NU)/sum(Ps); ### I got the following error
Undefined function 'times' for input arguments of type 'struct'.
Any help?
Cheers, Marcos
PS: I promised I will post the final solution to list. But I guess it
is more didactic if these little problems are solved before.
TY, again.
Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio
On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.
105.59.
How could I get similar results for each hippocampal subfield,
assuming I also generated all posterior*.mgz files corresponding to
each subfield?
I guess I should first
[Freesurfer] Cross-sectional v5.1 vs. Longitudinal v4.4
Dear All, If I had to choose between longitudinal processing v4.4 or cross-sectional processing v5.1 for analyzing longitudinal data, what processing stream should I choose? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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 measure the surface dimension in a mask image after mri_glmfit?
Got it. Thanks for the prompt answer! By the way, I tried mri_segstats with --accumulate flag, but it says option '--accumulate' is unknown. I don't seem to find it when I looked up mri_segstas --help either. On Tue, Jun 11, 2013 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Right, so in this case, the NVoxels column is the number of vertices, the Mean column is the average surface area of the vertices in the mask. You can force it to compute the total surface area by adding the --accumulate flag. Or you can multiple the mean by the number of vertices. doug On 06/11/2013 04:55 PM, Glen Lee wrote: Hi Doug -- I copied and pasted the summary file below. It looks like mask.mgh was treated as volumetric image. Also I'm not sure how to interpret TableCol. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ # cmdline mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat # sysname Linux # hostname rage.uphs.upenn.edu http://rage.uphs.upenn.edu # machine x86_64 # user gel # anatomy_type volume # # SegVolFile mask.mgh # SegVolFileTimeStamp 2013/06/05 14:50:24 # InVolFile /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area # InVolFileTimeStamp 2013/05/22 16:49:43 # InVolFrame 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 1 # NTableCols 9 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8183781837.0 Seg0001 0.3836 0. 0.1297 1.1861 1.0563 On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Did you look in the summary file? If you have questions about that, can you send it? doug On 06/11/2013 11:34 AM, Glen Lee wrote: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: what is your full command line? On 6/11/13 10:04 AM, Glen Lee wrote: thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 tel:1%2081837%20%2081837 tel:1%20%C2%A0%2081837%20%C2%**A081837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas 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 wrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o
