Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

nu_correct problem
by zach.petr＠post.cz 18 Jan '13

18 Jan '13

I tried on another standar PC (4 core processor) with XP Win recon-all in VirtualBox (latest edition) running Ubuntu. I attach file folder with patient brain - first in VirtualBox as described and then in command line of terminal Ubuntu window: sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder Then I convert original TrioTim scanner files using mri_convert -it IMA -ot mgz filename foldername.mgz * here is slight problem - recon log shows that mri_convert recognizes itself that although my brain files are labeled as IMA that they are not old Siemens files, so that it unpacks them as DICOM and suggests that if it fails I should run mri_convert as DICOM But after all mri_convert succesfully writes foldername.mgz file as a result of conversion in foldername directory Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 Now -cw256 was suggested in another error run because files do not fit in 256 matrix Recon stops and sayz no 001.mgz files in /mri/orig directory So I copy converted foldername.mgz from foldername directory into /mri/orig directory and rename it to 001.mgz *now here is my question: do all people get 001.mgz file the same way as me? Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with error at nu_correct as you can see in attached recon-all.log file Petr

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Freesurfer vertex wise area reference
by MAHINDA YOGARAJAH 17 Jan '13

17 Jan '13

Hi, Sorry to be a little more specific - I am aware of freesurfer area references such as the WInkler reference but basically wanted a few lines, and the most appropriate references, that summarises the technical approach used for group area comparisons in qdec (using updated mris_preproc), and simple ROI group area comparisons. Thanks, Mahinda

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Merging .annot files
by Chris McNorgan 17 Jan '13

17 Jan '13

Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot files: ?h.myaparcP1_16.annot, ?h.myaparcP17_28.annot, and ?h.myaparcP29_66.annot, for each of lh and rh. Each of these .annot files label the entire cortical surface, but each of the 36 major anatomical regions (e.g., posteriorcingulate) for each hemisphere are further subdivided in only one of the three .annot files; the other two files use the original definition of the major region. In other words, in order to use these .annot files to work with the Lausanne sub-parcellations for the entire cortical surface, one has to run the same procedure using each of the 3 .annot files, and then figure out which .annot file provided the desired information. I was wondering whether it is possible to merge the three annot files to create a single .annot file for each hemisphere in which ALL of the 36 major anatomical regions have been subdivided, rather than three files containing parcellations of different subsets of these regions? Though I have been using scripts to sift through multiple sets of results to find what I'm looking for, some manual chores would be easier if I only had to work with a single file. The fact that the same vertices are labeled in all files (but are given the macro-region label in 2 files, and the sub-parcelation label in 1 file) makes me think that it's not a simple matter of concatenating the annotation files. Thanks, Chris

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problem with AutoReco3 mapping
by jonwieser＠netzero.net 17 Jan '13

17 Jan '13

I did an AutoRecon3 on a brain and when i viewed the results. it failed to classify some the tgray and white matter in the left hemisphere. the area misses is on the extreme left side of the brain, within 10 mm of the left side of the hemisphere. are there some arguments i change change to fix this. Jon Wieser jonwieser(a)netzero.com "When the going gets tough, switch to power tools." - Red Green ____________________________________________________________ One Trick to Stay Asleep If you struggle to fall asleep, or stay asleep, try this&#8230 http://thirdpartyoffers.netzero.net/TGL3241/50f85712990b57112b48st01duc

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Re: [Freesurfer] nu_correct problem (fwd)
by Louis Nicholas Vinke 17 Jan '13

17 Jan '13

Please remember to cc the list. ---------- Forwarded message ---------- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.petr(a)post.cz To: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web page (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, Documentation) I´ll send recon-all.log file later on I have it on another PC. Orig.mgz file - thats also problem. What I did: when running recon-all -subjid name -autorecon1 I get error: no /mri/orig/orig.mgz file. I looked into patients /mri directory and this path and file is not there. So that I created directory /orig in /mri and copied there converted patient.mgz file there and renamed it to orig.mgz. So that I have /subject/patient/mri/orig/orig.mgz. Maybe thats what is wrong? How do you get normally orig.mgz file? Thanks, Petr ---------- Původní zpráva ---------- Od: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> Datum: 16. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated prior to the mri_nu_correct.mni step to see if it looks reasonable? -Louis On Wed, 16 Jan 2013, zach.petr(a)post.cz wrote: > > > Dear members, > > when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu_correct. This happens for > DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? > > Thanks much, Petr Zach > > > 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.

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edit or not to edit?
by Miro Drahos 17 Jan '13

17 Jan '13

Hi FreeSurfer folks, we are about to process about 120 images with FS v5.1 and stand in front of a decision whether to do manual intervention or use the results from fully-automated FS run. We intend to use the volume, thickness, area, curvature measures of subcortical and cortical regions and were hoping to receive some advice on this dilemma: /to edit / or/not to edit/? Our data is decent quality, of healthy children (6-9 years old) and adults, acquired on 3T GE scanner, FSPGR sequence, with TI=400ms, TR=8.5ms, TE=3.4ms, flip angle=15deg, resolution 0.86 x 0.86 x 1.2mm, one scan per subject. I understand that visual inspection of the results is necessary in either case. If there were gross errors detected, would you advise to exclude the subject from analysis or rather do manual editing on these subjects that need it? Any and all thoughts or comments that could help us with the decision are most appreciated! Thank you! Miro Drahos http://brainlens.org

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long_mris_slopes / mris_calc problem
by O'Shea,Andrew 17 Jan '13

17 Jan '13

Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/02031… However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew

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WM of lobes
by Gabriel Gonzalez Escamilla 17 Jan '13

17 Jan '13

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Re: [Freesurfer] A question regarding volume calculation
by Douglas N Greve 16 Jan '13

16 Jan '13

No, the subcortical calculation sums the number of voxels. For voxels on the edge of a structure, there is a partial volume calculation based on the intensity of the voxel and the mean intensities of the adjacent structures. doug On 01/16/2013 05:52 PM, KimMJ wrote: > > > ------------------------------------------------------------------------ > Dear Dr. Greve > > Thanks so much for your quick and clear response. > One additional question here. > Is this volume calculation method you have mentioned also applied to > volume measurement of subcortical GM structure (in addition to > cortical GM volume)? > > Thank you again > Kim > > > > Date: Tue, 15 Jan 2013 23:16:04 -0500 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] A question regarding volume calculation > > Hi Kim, yes it is surface area times thickness. A volume at each > vertex is computed as the average area of the triangles around the > vertex times the thickness at that vertex. The volume of a > parcellation is then the sum of the volumes of the vertices in that > parcellation. > doug > > > On 1/15/13 9:03 PM, KimMJ wrote: > > Dear experts > > > I'm currently preparing a paper using the results of automatic > volumetric segmentation of subcortical and cortical grey matter > structures from aseg.stats and aparc.stats files. > I have cited previous article by Desikan RS, et al (Neuroimage > 2006;31:968-980) for the cortical GM volumetric segmentation, and > Fischl B, et al (Neuron 2002;33:341-355) for the subcortical GM > volumetric segmentation. > At this point, my question is how volumes of these structures > calculated. Is this volume of each GM structure based on surface > area multiplied by cortical thickness? > > Apology for the newbie's question. > Thank you in advance for your help. > > Kim MJ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and > the e-mail contains patient information, please contact the Partners > Compliance HelpLine at http://www.partners.org/complianceline . If the > e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center 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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Re: [Freesurfer] separate FSAverages and surface-based ROIs
by Douglas N Greve 16 Jan '13

16 Jan '13

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>> 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> > > 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> > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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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Freesurfer January 2013