Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Trying to email out on the FreeSurfer mailing list
by Susan Kuo 07 Feb '13

07 Feb '13

Hi, I've been trying to email out for help to the FreeSurfer community, using the below addresses. However, I am not receiving my own email back, though I am a member of the mailing list via this email address. Can you tell me what I'm doing wrong? Thank you! Susan Kuo ---------- Forwarded message ---------- From: Susan Kuo <susan.kuo.run(a)gmail.com> Date: Wed, Feb 6, 2013 at 4:57 PM Subject: Troubleshooting the preproc To: ayendiki(a)nmr.mgh.harvard.edu Cc: freesurfer(a)nmr.mgh.harvard.edu Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c <config dmrirc>*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot <transform file> <input vector file> [<output vector file>]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K

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FDR threshold on functional data
by Susan Alice McLaughlin 06 Feb '13

06 Feb '13

Hi, I am looking at functional group surface data analyzed with mri_glmfit in tksurfer (using Freesurfer 4.1). I would like to threshold using FDR - but only within a specified label - and then see the resulting functional data map. Once I have the functional dta loaded as an overlay, I have been loading my label and marking the selected label under the Tools menu. I then set the threshold using FDR only on marked data. So far, so good. However, once this is done, I have not been able to see the thresholded functional map in the label; I can only the whole area in white, marked. How do I see my functional data map? I apologize for this simplistic question; I have not been able to find a solution looking through the tksurfer guides online or the mail archives. Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Re: [Freesurfer] aparc2aseg for an averaged subject
by Douglas N Greve 06 Feb '13

06 Feb '13

Hi Paul, try this cd $SUBJECTS_DIR/youraveragesubjectname mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon youraveragesubjectname doug On 02/04/2013 02:40 PM, Paul Beach wrote: > Hi Doug, > > Your suggestion to remove the 'unknown' label when using the > mris_label2annot command worked like a charm. Thanks! > > However, now I'm trying, as per your original advice, to re-run > mri_aparc2aseg in order to get my labels to fill out the entire > cortical ribbon (with the end goal of exporting these labels/ROIs to > AFNI). I tried this on my averaged subject (created with > 'make_average_subject') and it gave me the error that there is no > "ribbon.mgz" file in the mri folder. Upon checking the mri folder, > there is indeed no 'ribbon.mgz' file. > > Looking at the options for 'mri_aparc2aseg' on the wiki it doesn't > look like there's any way around this problem from that angle - at > least from the perspective of using my averaged subject. > > In the averaged subject's mri folder there are only the following files: > aseg.mgz > brain.mgz > orig.mgz > T1.mgz > brainmask.mgz > mni305.cor.mgz > p.aseg.mgz > > Interestingly, in the fsaverage subject there are ribbon.mgz files. Is > there a way to make a ribbon.mgz file for averaged subjects?? > > > Thanks, > Paul > > > > > On Thu, Jan 31, 2013 at 2:12 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, this mostly looks right. I think the problem may be that > you are including the unknown label on the command line. I think > that mris_label2annot will ignore the 0 inthe ctab file, which > means that it assign the first label passed (lh.unknown.label) to > the the first non-zero ROI in the ctab file (banksts). Try that > and see if it works. > doug > > > On 01/30/2013 03:03 PM, Paul Beach wrote: > > Hi Doug, > > I've been attempting to utilize the programs suggested by you > to create manual labels (ROIs) on the cortical surface of > tksurfer to be able to export certain ones to AFNI. The > problem I was having originally was that the cortical ribbon > was not fully covered by surface drawn labels that were > changed to volumes by MRI_label2vol. > > You suggested first using mri_annotation2label to extract the > labels within the aparc.annot files (left and right > hemispheres), putting my created labels into the same folder > (replacing, for example, the "insula" label with anterior, > middle, and posterior insula labels) and then using > mris_label2annotation to make a new annotated file to be sent > into a re-ran mri_aparc2aseg. > > The problem I'm running into now, after extracting all the > labels, putting in my own, and running mris_label2annotis that > the resultant annotation's labels are highly out of place and > disorganized. For example, the label for the cuneus is where > the corpus callosum is. > > I'm wondering if this has something to do with the order of > labels in the mris_label2annot script of possibly with my > .ctab file. The latter was created based on what I found here > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit> > on the Freesurfer wiki. I simply added my six manual > labels/ROIs at the end. I tried to use their GWFSAnnotToLUT > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=AttachF…> > program, but could not get it to work, so I'm not sure if the > .ctab file accurately represents tksurfer's Lookup Table. > > > I'm also not sure if it has something to do with overlapping > vertices of different labels. For example, will leaving the > "insula" label in mess things up when I also try to include > the anterior, middle, and posterior insula labels? If so, > would simply removing labels that overlap, vertex-wise, help? > > I have attached the setup of the .ctab file as well as my > mris_label2annot script. > > > Thanks for your advice, > Paul > > > On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach > <pabeach1(a)gmail.com <mailto:pabeach1@gmail.com> > <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote: > > Thanks for your help! > > > > On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > mri_annotation2label breaks them appart > mris_label2annot puts them back together again > doug > > On 01/22/2013 11:09 AM, Paul Beach wrote: > > Hi Doug, > > Thank you for this. However, can you give me a > hint as to > how I can go about breaking apart the aparc.annot > files > into their constituent label files? Are there a > particular > commands for doing this and eventually recombining the > labels into the overall aparc.annot file? > > > Thanks! > > > > On Wed, Jan 16, 2013 at 3:15 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > The "annotation" is the name we give to a surface > segmentation > (eg, lh.aparc.annot). You can break lh.aparc.annot > into its > constituent label files. You can then replace the > insula label > file with posterior and anterior labels that you > create. You can > then recombine the labels back into a new > annotation. > Once you > have the new annotation, you can run > mri_aparc2aseg to > map the > annotation into the volume. This method will > do better > at filling > in the cortical ribbon than mri_surf2vol or > mri_label2vol. > > doug > > > > On 01/16/2013 01:25 PM, Paul Beach wrote: > > Hi Doug, > > Thanks a lot for the reply. I'm relatively > new to > freesurfer > and it's great to see such a helpful > community. > > I'm a little fuzzy on what you mean with > your second > suggestion, related to the manual ROI > creation/export to AFNI. > Could you explain a bit more about > creating "a new > annotation > and then run mri_aparc2aseg." > > First, I'm not sure what you mean by "new > annotation." > > Second, my understanding is that > mri_aparc2aseg > normally deals > with ROIs in the LUT. However, looking at > the wiki > for this > command, it seems as though I can utilize my > created label > using the "--annot argName" option. > How does this look: > mri_aparc2aseg --s [subj] --annot > lh.aIns.label > --o lh.aIns_aparc > > > Cheers, > Paul > > > > On Wed, Jan 16, 2013 at 10:56 AM, Douglas > N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > Hi Paul, > > On 01/16/2013 10:27 AM, Paul Beach wrote: > > Hello, > > > > I have two issues, currently. > > > > First, I was wondering if it would be > possible to create > separate > > FSAverage brains for different subject > groups. I am > working with > > healthy seniors and various stages of > Alzheimer's > disease, so > doing so > > would be very helpful from the > perspective > of not > conflating the > > differences in neuroanatomy between the > these groups. > One idea > we had > > was to create separate HOME > directories for > each group, > but we > wanted > > to know if there was an easier way. > I can't find > anything in the > > interwebs about this. > You can create your own fsaverage > subject using > make_average_subject. > Note that when you run recon-all it > registers > to the standard > fsaverage > space. If you want to register to a > different > space, you > will need to > re-run mris_register. Once you do > this, you > will not be > able to > compare > groups. > > > > Second, I utilize some ROIs that are not > specified by FS > (such as > > secondary somatosensory cortex and > anterior > vs. posterior > insula). My > > means of getting around this was to use > FSAverage and > tksurfer to > > hand-draw them, save them as > '.label' files, > map them to > individual > > subjects, and export them to AFNI > since much > of our > correlation > > analysis is done on that platform. > However, > I've noticed > that when I > > view these hand-drawn ROIs in AFNI > they only > show up at the > border of > > the gray and white matter, rather than > filling the > entirety of the > > gray matter. Note that this problem > does not > occur for > ROIs in the > > look up table (like the caudal ACC). > Exporting these to AFNI > gives you > > a nice ROI that fills all the gray > matter in > the defined > region. > Try using --proj frac 0 1 .1 with > mri_label2vol. Or you > can create > a new > annotation and then run > mri_aparc2aseg. The > 2nd method > works a little > better since the 1st method can leave > some holes. > > doug > > > > _Code I'm using_: > > For the latter problem, what I first > use is > mri_label2label to > map the > > fsaverage-based ROI onto individual > subjects, for > example with the > > left anterior insula, before using > mri_label2vol: > > *mri_label2label --srclabel > lh.aIns.label > --srcsubject > fsaverage > > --trglabel lh.aIns.label > --trgsubject [subj] > --regmethod > surface > > --hemi lh* > > > > *mri_label2vol --label > ../label/lh.aIns.label --regheader > > aparc+aseg.mgz --o gmroi_volume.nii.gz > --temp orig/001.mgz* > > > > > > Then I copy the new volume file to their > AFNI folder, > rename it, and > > run my correlation analysis on them. > > > > Note, that for those ROIs that are > in the > look up table > (those > > parcellated by freesurfer) I simply use > mri_label2vol before > > extracting them using 3dcalc (for > example, > the caudal > anterior > > cingulate)... > > *mri_label2vol --seg aparc+aseg.mgz > --regheader > aparc+aseg.mgz --o > > gmroi_volume.nii.gz --temp orig/001.mgz* > > > > *3dcalc -a gmroi_volume.nii.gz -expr > 'equals(a,1002)' > -prefix > > ROI_FS_lh.caudalACC.nii.gz* > > > > > > > > tl:dr > > Is it possible to "easily" create > multiple > FSAverages > based on > > selected subjects (in my case, subject > groups separated by > disease state)? > > > > and > > > > Does anyone have any advice on how > to get > hand-drawn > surface-based > > ROIs from Freesurfer's tksurfer into > AFNI > that full > cover the > entirety > > of the gray matter? > > > > > > Cheers and thanks! > > -- > > Paul Beach > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > > -- Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist > Association, MSU COM > Chapter > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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/ > > > > > -- Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist > Association, MSU > COM Chapter > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU > COM Chapter > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM > Chapter > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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: 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/ > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Difficult results from our PD data
by Berg, S.F. van den 06 Feb '13

06 Feb '13

Dear Freesurfer experts, We investigated the relation between cortical thickness and performance on several cognitive tasks within a large group of Parkinson’s disease patients, but are slightly puzzled by the results. We obtained several, both in the vertex-wise analysis in qdec and in the SPSS analysis in the a-priori parcelated areas, negative correlations (i.e. better performance relates to a thinner cortical area) for all our neuropsychological tasks. These negative correlations were unexpected and we are having a hard time interpreting them. After correcting for multiple comparisons, all effects failed to reach the statistical threshold, rendering no results at all. When we compared our patient group on a structural level with healthy controls, we did find expected results that made sense. We also ran the exact same analyses (same group, same data) in VBM and there found several positive task-related correlations in expected areas. We noticed that in previous literature almost no studies investigated the relation between cortical thickness and cognitive task-performance. This made us wonder whether Freesurfer is suited for these correlation-based analyses, or is it better to be used in between group analyses? And do you have any idea on how to explain our negative correlations? Is it possible we might have done something wrong? Many thanks, Stan

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ROI analysis and whitening in fsfast
by Clark Fisher 06 Feb '13

06 Feb '13

Hi everyone, In a previous discussion on this list (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html) Pablo Polosecki was asking the best way to perform hypothesis testing using functional data within an ROI. The final opinion was that it was best to average all of the time courses in the ROI, and re-run the analysis from scratch, so that all of the appropriate whitening, etc. occurred. I was considering doing this, creating a small volume (say, 10 voxels total) that had each voxel holding the average time course from one of 10 ROIs. I would then set up and run a usual fsfast analysis using these tiny volumes. I am using freesurfer 4.5. I have a few questions. 1) Is this reasonable? 2) One area where I expect to run into problems is with the whitening. If I set -acfbins to the total number of my dummy voxels, and -acffwhm to 0, will this use the autocorrelation function of the average timecourse within each individual ROI? Is that an appropriate approach? How sensitive will this be to the number of actual voxels averaged to get each ROI (for instance, would this bias me to finding more significant results in ROIs containing fewer voxels?). 3) Are there other steps that depend upon the spatial arrangement of voxels that I am forgetting, and will these steps choke on these small volumes (or worse, fail in silent but pernicious ways). Thanks for all of the help, Clark

2 1

Xhemi questions
by Gabriel Gonzalez Escamilla 06 Feb '13

06 Feb '13

2 1

Problem with flip4fsl
by Susan Kuo 06 Feb '13

06 Feb '13

Hi FreeSurfer community, I am trying to run 'trac-all -corr -c <config file>' on the tutorial data, specifically for the single subject: Diff001. To start from 'scratch', I've deleted all but the './scripts' and the './orig' directories in the Diff001 parent folder. When I run the following command: > trac-all -corr -c <config file> I receive the following error: ERROR BEGINS----> flip4fsl /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz x -y z /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz Cannot open volume /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip for reading! ----> ERROR ENDS Looking in my 'Diff001/dmri' directory, I cannot locate a 'dwi_orig_flip.nii.gz' file. I assume this is where the script breaks. I tried to run the 'flip4fsl' command singly, but received the same error. I'm working on a: 3.2.0-35-generic #55-Ubuntu SMP Wed Dec 5 17:42:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux I've unsuccessfully searched through the mailing list archive to find if others had encountered the same issue previously. Does anybody have any suggestions? Thanks! Susie

1 0

Qdec
by Franklin, Crystal G 06 Feb '13

06 Feb '13

Freesurfer, I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences? Thank you, Crystal

2 6

invalid=766 recon-all
by stdp82＠virgilio.it 06 Feb '13

06 Feb '13

Hi list, I'm running :recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_sub001In bold the error that I'm visualizing: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01Actual FREESURFER_HOME /Applications/freesurferDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001\n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz \nmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.998454, 0.00426797, -0.0554224)j_ras = (0.0151969, 0.980022, -0.198308)k_ras = (-0.0534688, 0.198844, 0.978572)writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz...#--------------------------------------------#@# MotionCor Mon Feb 4 20:34:08 CET 2013Found 1 runs/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgzChecking for (invalid) multi-frame inputs...WARNING: only one run found. This is OK, but motioncorrection cannot be performed on one run, so I'llcopy the run to rawavg and continue.\n cp /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz \n/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001\n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform \nmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.998454, 0.00426797, -0.0554224)j_ras = (0.0151969, 0.980022, -0.198308)k_ras = (-0.0534688, 0.198844, 0.978572)Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels.Data is conformed to 1 mm size and 256 voxels for all directionschanging data type from float to uchar (noscale = 0)...MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz...\n mri_add_xform_to_header -c /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz \nINFO: extension is mgz#--------------------------------------------#@# Talairach Mon Feb 4 20:34:17 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n#--------------------------------------------#@# Talairach Failure Detection Mon Feb 4 20:34:49 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \ntalairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4903, pval=0.1531 >= threshold=0.0050)\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log \nTalAviQA: 0.96699z-score: -2#--------------------------------------------#@# Nu Intensity Correction Mon Feb 4 20:34:50 CET 2013\n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 \n/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/Applications/freesurfer/bin/mri_nu_correct.mni--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2nIters 2$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64Mon Feb 4 20:34:50 CET 2013Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nschmans@W0084482 (i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56tmpdir is ./tmp.mri_nu_correct.mni.17691/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mrimri_convert orig.mgz ./tmp.mri_nu_correct.mni.17691/nu0.mnc -odt floatmri_convert orig.mgz ./tmp.mri_nu_correct.mni.17691/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from orig.mgz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 1.86265e-09, 7.45058e-09)j_ras = (1.11759e-08, -5.96046e-08, -1)k_ras = (1.86265e-09, 1, -2.98023e-08)changing data type from uchar to float (noscale = 0)...writing to ./tmp.mri_nu_correct.mni.17691/nu0.mnc... --------------------------------------------------------Iteration 1 Mon Feb 4 20:34:53 CET 2013nu_correct -clobber ./tmp.mri_nu_correct.mni.17691/nu0.mnc ./tmp.mri_nu_correct.mni.17691/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17691/0/[Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] [2013-02-04 20:34:53] running: /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17691/0/ ./tmp.mri_nu_correct.mni.17691/nu0.mnc ./tmp.mri_nu_correct.mni.17691/nu1.imp Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Number of iterations: 44 CV of field change: 0.000967614[Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] [2013-02-04 20:35:16] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17691/nu0.mnc ./tmp.mri_nu_correct.mni.17691/0//template.mnc Transforming slices:......................................................................................DoneNot implemented yet in cache_volume_range_has_changed()Transforming slices:................................................................................................................................................................................................................................................................Done --------------------------------------------------------Iteration 2 Mon Feb 4 20:35:21 CET 2013nu_correct -clobber ./tmp.mri_nu_correct.mni.17691/nu1.mnc ./tmp.mri_nu_correct.mni.17691/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17691/1/[Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] [2013-02-04 20:35:21] running: /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17691/1/ ./tmp.mri_nu_correct.mni.17691/nu1.mnc ./tmp.mri_nu_correct.mni.17691/nu2.imp Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Number of iterations: 20 CV of field change: 0.000999692[Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] [2013-02-04 20:35:32] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17691/nu1.mnc ./tmp.mri_nu_correct.mni.17691/1//template.mnc Transforming slices:......................................................................................DoneNot implemented yet in cache_volume_range_has_changed()Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17691/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $cwd /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mricmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17691/ones.mgz sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user Stefano input ./tmp.mri_nu_correct.mni.17691/nu2.mncframe 0nErode3d 0nErode2d 0output ./tmp.mri_nu_correct.mni.17691/ones.mgzBinarizing based on thresholdmin -1max +infinitybinval 1binvalnot 0Found 16777216 values in rangeCounting number of voxelsFound 16777216 voxels in final maskmri_binarize donemri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17691/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17691/input.mean.dat sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoLoading ./tmp.mri_nu_correct.mni.17691/ones.mgzLoading orig.mgzVoxel Volume is 1 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentationsComputing spatial average of each frame 0Writing to ./tmp.mri_nu_correct.mni.17691/input.mean.datmri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17691/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17691/output.mean.dat sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoLoading ./tmp.mri_nu_correct.mni.17691/ones.mgzLoading ./tmp.mri_nu_correct.mni.17691/nu2.mncVoxel Volume is 1 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentationsComputing spatial average of each frame 0Writing to ./tmp.mri_nu_correct.mni.17691/output.mean.datmris_calc -o ./tmp.mri_nu_correct.mni.17691/nu2.mnc ./tmp.mri_nu_correct.mni.17691/nu2.mnc mul .98419113815649368597Saving result to './tmp.mri_nu_correct.mni.17691/nu2.mnc' (type = MINC ) [ ok ]mri_convert ./tmp.mri_nu_correct.mni.17691/nu2.mnc nu.mgz --like orig.mgzmri_convert ./tmp.mri_nu_correct.mni.17691/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from ./tmp.mri_nu_correct.mni.17691/nu2.mnc...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 1.86265e-09, 7.45058e-09)j_ras = (1.11759e-08, -5.96046e-08, -1)k_ras = (1.86265e-09, 1, -2.98023e-08)INFO: transform src into the like-volume: orig.mgzwriting to nu.mgz...mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgztype change took 0 minutes and 6 seconds.mapping (14, 168) to ( 3, 110) Mon Feb 4 20:36:08 CET 2013mri_nu_correct.mni done#--------------------------------------------#@# Intensity Normalization Mon Feb 4 20:36:08 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n mri_normalize -g 1 nu.mgz T1.mgz \nusing max gradient = 1.000reading from nu.mgz...normalizing image...talairach transform 1.063 -0.036 0.068 -2.289; 0.026 1.120 -0.133 -8.875;-0.088 0.148 1.191 -31.505; 0.000 0.000 0.000 1.000;INFO: Modifying talairach volume c_(r,a,s) based on average_305building Voronoi diagram...performing soap bubble smoothing...3d normalization pass 1 of 2building Voronoi diagram...performing soap bubble smoothing...3d normalization pass 2 of 2building Voronoi diagram...performing soap bubble smoothing...writing output to T1.mgz3D bias adjustment took 2 minutes and 50 seconds.MRIsplineNormalize(): npeaks = 19Starting OpenSpline(): npoints = 19white matter peak found at 111white matter peak found at 109gm peak at 84 (84), valley at 71 (71)csf peak at 40, setting threshold to 69white matter peak found at 111white matter peak found at 110gm peak at 85 (85), valley at 57 (57)csf peak at 33, setting threshold to 67#--------------------------------------------#@# Skull Stripping Mon Feb 4 20:38:59 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n mri_em_register -skull nu.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta \naligning to atlas containing skull, setting unknown_nbr_spacing = 5reading 1 input volumes...logging results to talairach_with_skull.logreading '/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0average std = 23.1 using min determinant for regularization = 53.40 singular and 5702 ill-conditioned covariance matrices regularizedreading 'nu.mgz'...freeing gibbs priors...done.bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)************************************************spacing=8, using 3481 sample points, tol=1.00e-05...************************************************register_mri: find_optimal_transformfind_optimal_transform: nsamples 3481, passno 0, spacing 8resetting wm mean[0]: 117 --> 126resetting gm mean[0]: 74 --> 74input volume #1 is the most T1-likeusing real data threshold=13.0skull bounding box = (48, 49, 39) --> (210, 226, 213)using (102, 108, 126) as brain centroid...mean wm in atlas = 126, using box (82,86,105) --> (121, 129,147) to find MRI wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.200scaling channel 0 by 1.2initial log_p = -10395.9************************************************First Search limited to translation only.************************************************Found translation: (-7.4, -13.1, -6.3): log p = -10344.984****************************************Nine parameter search. iteration 0 nscales = 0 ...****************************************Result so far: scale 1.000: max_log_p=-10343.3, old_max_log_p =-10345.0 (thresh=-10334.6) 0.983 0.131 0.129 -29.663;-0.129 0.991 -0.017 7.223;-0.140 0.000 1.066 -2.456; 0.000 0.000 0.000 1.000;reducing scale to 0.2500****************************************Nine parameter search. iteration 1 nscales = 1 ...****************************************Result so far: scale 0.250: max_log_p=-10331.8, old_max_log_p =-10343.3 (thresh=-10332.9) 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000;****************************************Nine parameter search. iteration 2 nscales = 1 ...****************************************Result so far: scale 0.250: max_log_p=-10331.8, old_max_log_p =-10331.8 (thresh=-10321.5) 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000;reducing scale to 0.0625****************************************Nine parameter search. iteration 3 nscales = 2 ...****************************************Result so far: scale 0.062: max_log_p=-10331.8, old_max_log_p =-10331.8 (thresh=-10321.5) 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000;min search scale 0.025000 reached***********************************************Computing MAP estimate using 3481 samples...***********************************************dt = 5.00e-06, momentum=0.80, tol=1.00e-05l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 1.00929 0.06752 0.12102 -29.00327;-0.08608 0.98449 0.16623 -21.03892;-0.11966 -0.16323 1.07352 15.91519; 0.00000 0.00000 0.00000 1.00000;nsamples 3481Quasinewton: input matrix 1.00929 0.06752 0.12102 -29.00327;-0.08608 0.98449 0.16623 -21.03892;-0.11966 -0.16323 1.07352 15.91519; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10331.8 tol 0.000010Resulting transform: 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10331.8 (old=-10395.9)transform before final EM align: 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. **************************************************dt = 5.00e-06, momentum=0.80, tol=1.00e-07l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 1.00929 0.06752 0.12102 -29.00327;-0.08608 0.98449 0.16623 -21.03892;-0.11966 -0.16323 1.07352 15.91519; 0.00000 0.00000 0.00000 1.00000;nsamples 382743Quasinewton: input matrix 1.00929 0.06752 0.12102 -29.00327;-0.08608 0.98449 0.16623 -21.03892;-0.11966 -0.16323 1.07352 15.91519; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1145838.5 tol 0.000000final transform: 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta...registration took 14 minutes and 43 seconds.\n mri_watershed -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n Mode: T1 normalized volumeMode: Use the information of atlas (default parms, --help for details)gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0 *********************************************************The input file is T1.mgzThe output file is brainmask.auto.mgzWeighting the input with atlas information before watershed *************************WATERSHED**************************Sorting... first estimation of the COG coord: x=131 y=121 z=129 r=76 first estimation of the main basin volume: 1870432 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=96, y=112, z=94, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percentdone.Analyze... main basin size=361193305 voxels, voxel volume =1.000 = 361193305 mmm3 = 361193.312 cm3done.PostAnalyze...Basin Prior 44 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basindone.Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=130, z=117, r=9449 iterations^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = -1072089698 RIGHT_CER CSF_MIN=0, CSF_intensity=25, CSF_MAX=47 , nb = -1035635533 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = -1086068051 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 1065522184 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = -1036263885 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 387 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 22, 18, 6, 87 after analyzing : 18, 22, 25, 38 RIGHT_CER before analyzing : 47, 40, 17, 93 after analyzing : 35, 40, 40, 53 LEFT_CER before analyzing : 23, 65, 82, 90 after analyzing : 23, 76, 82, 79 RIGHT_BRAIN before analyzing : 21, 22, 28, 85 after analyzing : 21, 26, 28, 40 LEFT_BRAIN before analyzing : 22, 20, 13, 89 after analyzing : 20, 23, 25, 39 OTHER before analyzing : 19, 16, 6, 87 after analyzing : 16, 22, 25, 38 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION*********************curvature mean = -0.013, std = 0.009curvature mean = 74.494, std = 5.862 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 6.45, sigma = 10.96 after rotation: sse = 6.45, sigma = 10.96Localization of inacurate regions: Erosion-Dilation steps the sse mean is 7.59, its var is 13.01 before Erosion-Dilatation 5.37% of inacurate vertices after Erosion-Dilatation 8.52% of inacurate vertices Validation of the shape of the surface done.Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION********Compute Local values csf/grayFine Segmentation...38 iterations mri_strip_skull: done peeling brain Brain Size = 1931109 voxels, voxel volume = 1.000 mm3 = 1931109 mmm3 = 1931.109 cm3 ******************************Saving brainmask.auto.mgzdone\n cp brainmask.auto.mgz brainmask.mgz \n#-------------------------------------#@# EM Registration Mon Feb 4 20:54:11 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \naligning to atlas containing skull, setting unknown_nbr_spacing = 3using MR volume brainmask.mgz to mask input volume...reading 1 input volumes...logging results to talairach.logreading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0average std = 6.9 using min determinant for regularization = 4.70 singular and 1812 ill-conditioned covariance matrices regularizedreading 'nu.mgz'...freeing gibbs priors...done.bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros)************************************************spacing=8, using 2772 sample points, tol=1.00e-05...************************************************register_mri: find_optimal_transformfind_optimal_transform: nsamples 2772, passno 0, spacing 8resetting wm mean[0]: 102 --> 107resetting gm mean[0]: 64 --> 64input volume #1 is the most T1-likeusing real data threshold=20.0skull bounding box = (61, 59, 39) --> (198, 225, 209)using (107, 114, 124) as brain centroid...mean wm in atlas = 107, using box (90,94,103) --> (123, 134,144) to find MRI wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.019scaling channel 0 by 1.01905initial log_p = -7523.2************************************************First Search limited to translation only.************************************************Found translation: (-4.0, -8.5, -13.1): log p = -7211.725****************************************Nine parameter search. iteration 0 nscales = 0 ...****************************************Result so far: scale 1.000: max_log_p=-7211.7, old_max_log_p =-7211.7 (thresh=-7204.5) 1.000 0.000 0.000 -3.977; 0.000 1.000 0.000 -8.523; 0.000 0.000 1.000 -13.068; 0.000 0.000 0.000 1.000;reducing scale to 0.2500****************************************Nine parameter search. iteration 1 nscales = 1 ...****************************************Result so far: scale 0.250: max_log_p=-7125.6, old_max_log_p =-7211.7 (thresh=-7204.5) 0.976 0.068 0.060 -16.633;-0.069 1.052 -0.073 2.558;-0.065 0.065 0.996 -8.572; 0.000 0.000 0.000 1.000;****************************************Nine parameter search. iteration 2 nscales = 1 ...****************************************Result so far: scale 0.250: max_log_p=-7125.6, old_max_log_p =-7125.6 (thresh=-7118.5) 0.976 0.068 0.060 -16.633;-0.069 1.052 -0.073 2.558;-0.065 0.065 0.996 -8.572; 0.000 0.000 0.000 1.000;reducing scale to 0.0625****************************************Nine parameter search. iteration 3 nscales = 2 ...****************************************Result so far: scale 0.062: max_log_p=-7094.4, old_max_log_p =-7125.6 (thresh=-7118.5) 0.976 0.085 0.059 -18.687;-0.085 1.055 -0.075 3.581;-0.065 0.065 0.996 -9.040; 0.000 0.000 0.000 1.000;****************************************Nine parameter search. iteration 4 nscales = 2 ...****************************************Result so far: scale 0.062: max_log_p=-7093.2, old_max_log_p =-7094.4 (thresh=-7087.3) 0.976 0.085 0.059 -18.687;-0.085 1.057 -0.075 3.311;-0.065 0.065 0.996 -9.040; 0.000 0.000 0.000 1.000;min search scale 0.025000 reached***********************************************Computing MAP estimate using 2772 samples...***********************************************dt = 5.00e-06, momentum=0.80, tol=1.00e-05l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;nsamples 2772Quasinewton: input matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 7093.2 tol 0.000010Resulting transform: 0.976 0.085 0.059 -18.687;-0.085 1.057 -0.075 3.311;-0.065 0.065 0.996 -9.040; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7093.2 (old=-7523.2)transform before final EM align: 0.976 0.085 0.059 -18.687;-0.085 1.057 -0.075 3.311;-0.065 0.065 0.996 -9.040; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. **************************************************dt = 5.00e-06, momentum=0.80, tol=1.00e-07l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;nsamples 312841Quasinewton: input matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;dfp_em_step_func: 008: -log(p) = 844596.4after pass:transform: ( 0.98, 0.09, 0.06, -18.69) ( -0.08, 1.06, -0.07, 3.31) ( -0.07, 0.06, 1.00, -9.04) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 844596.4 tol 0.000000final transform: 0.984 0.092 0.065 -18.687;-0.079 1.063 -0.069 3.311;-0.066 0.064 0.996 -9.040; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta...registration took 14 minutes and 23 seconds.#--------------------------------------#@# CA Normalize Mon Feb 4 21:08:34 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz \nwriting control point volume to ctrl_pts.mgzusing MR volume brainmask.mgz to mask input volume...reading 1 input volumesreading atlas from '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0reading transform from 'transforms/talairach.lta'...reading input volume from nu.mgz...resetting wm mean[0]: 102 --> 107resetting gm mean[0]: 64 --> 64input volume #1 is the most T1-likeusing real data threshold=20.0skull bounding box = (61, 59, 39) --> (198, 225, 209)using (107, 114, 124) as brain centroid...mean wm in atlas = 107, using box (90,94,103) --> (123, 134,144) to find MRI wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.019scaling channel 0 by 1.01905using 244171 sample points...INFO: compute sample coordinates transform 0.984 0.092 0.065 -18.687;-0.079 1.063 -0.069 3.311;-0.066 0.064 0.996 -9.040; 0.000 0.000 0.000 1.000;INFO: transform usedfinding control points in Left_Cerebral_White_Matter....found 41584 control points for structure...bounding box (124, 63, 35) --> (195, 177, 204)Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 182.02 of 1837 (0.1%) samples deletedfinding control points in Right_Cerebral_White_Matter....found 40735 control points for structure...bounding box (61, 61, 35) --> (132, 173, 203)Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 182.00 of 2081 (0.0%) samples deletedfinding control points in Left_Cerebellum_White_Matter....found 3012 control points for structure...bounding box (129, 138, 56) --> (176, 182, 110)Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 182.00 of 77 (0.0%) samples deletedfinding control points in Right_Cerebellum_White_Matter....found 2764 control points for structure...bounding box (79, 138, 52) --> (129, 178, 109)Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 182.00 of 99 (0.0%) samples deletedfinding control points in Brain_Stem....found 3520 control points for structure...bounding box (108, 135, 87) --> (142, 199, 122)Brain_Stem: limiting intensities to 100.0 --> 182.00 of 247 (0.0%) samples deletedusing 4341 total control points for intensity normalization...bias field = 0.965 +- 0.0752 of 4339 control points discardedfinding control points in Left_Cerebral_White_Matter....found 41584 control points for structure...bounding box (124, 63, 35) --> (195, 177, 204)Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 146.02 of 2231 (0.1%) samples deletedfinding control points in Right_Cerebral_White_Matter....found 40735 control points for structure...bounding box (61, 61, 35) --> (132, 173, 203)Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 146.00 of 2411 (0.0%) samples deletedfinding control points in Left_Cerebellum_White_Matter....found 3012 control points for structure...bounding box (129, 138, 56) --> (176, 182, 110)Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 146.011 of 109 (10.1%) samples deletedfinding control points in Right_Cerebellum_White_Matter....found 2764 control points for structure...bounding box (79, 138, 52) --> (129, 178, 109)Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 146.011 of 115 (9.6%) samples deletedfinding control points in Brain_Stem....found 3520 control points for structure...bounding box (108, 135, 87) --> (142, 199, 122)Brain_Stem: limiting intensities to 88.0 --> 146.08 of 315 (2.5%) samples deletedusing 5181 total control points for intensity normalization...bias field = 1.018 +- 0.05412 of 5149 control points discardedfinding control points in Left_Cerebral_White_Matter....found 41584 control points for structure...bounding box (124, 63, 35) --> (195, 177, 204)Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 140.02 of 2274 (0.1%) samples deletedfinding control points in Right_Cerebral_White_Matter....found 40735 control points for structure...bounding box (61, 61, 35) --> (132, 173, 203)Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 140.02 of 2331 (0.1%) samples deletedfinding control points in Left_Cerebellum_White_Matter....found 3012 control points for structure...bounding box (129, 138, 56) --> (176, 182, 110)Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 140.031 of 121 (25.6%) samples deletedfinding control points in Right_Cerebellum_White_Matter....found 2764 control points for structure...bounding box (79, 138, 52) --> (129, 178, 109)Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 140.028 of 144 (19.4%) samples deletedfinding control points in Brain_Stem....found 3520 control points for structure...bounding box (108, 135, 87) --> (142, 199, 122)Brain_Stem: limiting intensities to 84.0 --> 140.013 of 307 (4.2%) samples deletedusing 5177 total control points for intensity normalization...bias field = 1.015 +- 0.04314 of 5101 control points discardedwriting normalized volume to norm.mgz...writing control points to ctrl_pts.mgzfreeing GCA...done.normalization took 1 minutes and 49 seconds.#--------------------------------------#@# CA Reg Mon Feb 4 21:10:23 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z \nnot handling expanded ventricles...using previously computed transform transforms/talairach.ltarenormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500using MR volume brainmask.mgz to mask input volume...reading 1 input volumes...logging results to talairach.logreading input volume 'norm.mgz'...reading GCA '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0freeing gibbs priors...done.average std[0] = 5.0label assignment complete, 0 changed (0.00%)det(m_affine) = 1.06 (predicted orig area = 7.6)label assignment complete, 0 changed (0.00%)**************** pass 1 of 1 ************************setting smoothness coefficient to 0.039blurring input image with Gaussian with sigma=2.000...0000: dt=0.000, rms=0.876, neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 18445.328 ms0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19654.701 ms0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19650.012 ms0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19766.332 ms0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=7660005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=7660006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=7660007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=7660008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 Thanks, Stefano

2 1

Memory Consumption of GPU-assisted Freesurfer?
by Zhongtian Dai 06 Feb '13

06 Feb '13

Hi, I wonder how much graphic card memory is needed by the CUDA commands. We have two Quadro NVS 295's with 256MB memory and the CUDA commands all report "out of memory" errors. I know the cards are kind of outdated but I want to make sure a new card would meet the task before purchasing. A separate question is whether the current CUDA implementation supports spreading the work to multiple GPU's if they are present? Thanks. -- Zhongtian (Falcon) Dai University of Chicago

3 4

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Freesurfer February 2013