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Re: [Freesurfer] infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

I guess the problem is that those regions should not be out of bounds. Maybe I need to create a new Lookup Table for the infant mri's? Is that possible to do? On Wed, Jul 24, 2013 at 2:21 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Hi Mark, please post to the list and not to me. > thanks > doug > > On 07/24/2013 03:21 PM, Mark Plantz wrote: > >> I guess the problem is that those regions should not be out of bounds. >> Maybe I need to create a new Lookup Table for the infant mri's? Is that >> possible to do? >> >> >> On Wed, Jul 24, 2013 at 2:15 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> what is the problem exactly? The fact that there are red regions >> or that that the red regions are labeled as "Out of Bounds"? If >> the latter, you will need to create a LUT that matches your >> regions. the out of bounds means that the index in the volume does >> not match an index in the LUT. >> doug >> >> >> >> On 07/24/2013 01:26 PM, Mark Plantz wrote: >> >> Finally got the registration to work. However, it looks like >> the out of bounds regions (in red) are still present (even >> though the regions are well within our boundaries). Is that >> expected since they were labeled in the original segmentation >> volume? Is there anyway to correct those? >> >> Thanks for all of the help! >> >> - Mark >> p.s. I attached a picture of the original brain.mgz file >> viewed with the corrected segmentation volume >> >> >> On Wed, Jul 24, 2013 at 12:22 PM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Finally got the registration to work. However, it looks >> like the >> out of bound regions (in red) are still prevalent. Is that >> expected since they were present in the original segmentation >> volume? Would there be anyway to correct those? >> >> Thanks for all the help! >> >> - MP >> >> >> On Wed, Jul 24, 2013 at 11:11 AM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Nevermind, it turned out to be a permissions issue. >> Thanks! >> >> >> On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Thanks for the reply Doug. I recently ran the >> bbregister >> command and attempted to view the results using >> tkregister2. I received the following error: >> >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ tkregister2 --mov >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> --reg /Users/IngvalsonLab/Desktop/**register.dat >> --surf >> >> tkregister_tcl >> /Applications/freesurfer/**tktools/tkregister2.tcl >> INFO: no target volume specified, assuming >> FreeSurfer orig >> volume. >> target volume orig >> movable volume >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> reg file /Users/IngvalsonLab/Desktop/**register.dat >> LoadVol 1 >> ZeroCRAS 0 >> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 >> greve Exp $ >> Diagnostic Level -1 >> regio_read_register(): Undefined error: 0 >> Error reading subject from >> /Users/IngvalsonLab/Desktop/**register.dat >> ERROR: reading >> /Users/IngvalsonLab/Desktop/**register.dat >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ >> >> I do not believe it is a permissions issue? >> >> Could it simply be that the register was bad? Is >> there an >> easy way to open up the register.dat.mincost file >> to check >> the registration? >> >> Thanks again, >> >> MP >> >> >> On Tue, Jul 23, 2013 at 9:32 PM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> You can try using bbregister. Normally, you >> don't use >> bbregister on a segmentation, but the segmentation >> index numbers just happen to be "T1-weighted". >> doug >> ps. Please remember to copy the list when >> responding. >> thanks! >> >> >> >> On 7/23/13 9:51 AM, Mark Plantz wrote: >> >> Hi Doug, >> >> Sorry about that vague explanation. So >> I received >> a series of infant brain atlases from a >> UNC medical >> research group >> (http://www.med.unc.edu/bric/** >> ideagroup/free-softwares/unc-**infant-0-1-2-atlases<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…> >> ). >> I have a series of infant MRI's that I >> would like to >> segment (using the infant atlases, instead >> of the >> default adult atlas in FreeSurfer). >> >> As a preliminary step, I was attempting >> to check >> the alignment of one of the atlas files >> ('avgseg.mgz') with one of the input brains >> ('brain.mgz'). [I attached these two >> files, just in >> case]. >> >> So my command line would be: >> >> tkmedit $Subject brain.mgz -segmentation >> avgseg.mgz >> $FREESURFER_HOME/**FreeSurferColorLUT.txt >> >> The result was the previously attached >> image. I was >> just wondering if there is any way to >> shift the two >> images manually so the alignment is >> better? Or maybe >> the two files are simply not compatible >> with one another? >> >> Thanks for all the help! >> >> Best, >> >> Mark >> >> >> >> >> On Mon, Jul 22, 2013 at 3:53 PM, Douglas N >> Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> Hi Mark, I have no idea what you are >> doing. Can >> you send a command line? >> Are either of the images generated by FS? >> doug >> >> >> >> >> On 07/22/2013 03:56 PM, Mark Plantz wrote: >> > Hello FreeSurfers, >> > >> > I recently obtained a set of infant >> templates. Out of curiousity, >> > I decided to view one of the input >> brains with >> the provided segmented >> > volume file. It appears that there >> is some >> misalignment. I wouldn't >> > expect the alignment to be perfect, >> since I am >> basically overlaying an >> > average of multiple brains onto one. >> However, >> it looks like this >> > misalignment may be caused by >> either: 1.) the >> segmentation volume file >> > being shifted down or 2.) the slices >> not lining >> up properly (i.e. one >> > file starts before the other). >> > >> > Any ideas what could cause a >> problem like >> this? Could it be that >> > the segmented files are simply not >> compatible >> with FreeSurfer? >> > >> > Thanks for the help, >> > >> > Mark >> > >> > >> > >> > >> ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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<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: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >> <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/ <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<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<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 <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >> <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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

3 7

displaying labels from old session onto new session
by Bianca van Kemenade 29 Jul '13

29 Jul '13

Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca

3 17

Processing Multiple Subjects
by Michael Kranz 29 Jul '13

29 Jul '13

Hi all, If I process more subjects than the recommended amount given my number of cores and memory, will this affect the stats/surfaces or just slow the process down? I'm asking due to the sensitivity of workstations and also I seem to be getting slightly different stats sometimes when I re-submit to recon-all but haven't pin pointed the reason yet. Thanks, Mike

2 1

function that do the same step like qcache?
by fatma zribi 29 Jul '13

29 Jul '13

Dear Bruce, Would you mind tell me if there is a function of freesurfer that I can use to do the same step of qcache to smooth and interpolate in the fsaverage one subject with mri_surf2surf I can smooth only or align one subject with an average. thank you for you help. with best regards, Fatma

2 3

Error
by Muhammad Naveed Iqbal Qureshi 29 Jul '13

29 Jul '13

Dear Community, I got the following error every time I try to calculate the cortical thickness of my MRI data: bmssa-desktop:~> recon-all -i /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm -subject sub02 -all -qcache & WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/bmssa/freesurfer/subjects Actual FREESURFER_HOME /home/bmssa/freesurfer Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/bmssa/freesurfer/subjects/sub02 mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz ERROR: cannot determine file type for /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub02 exited with ERRORS at Mon Jul 29 14:10:40 KST 2013 For more details, see the log file /home/bmssa/freesurfer/subjects/sub02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Please guide me how to rectify this error. I have used the same command for another dataset and it was working perfectly fine. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi(a)hotmail.com URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to

2 1

dPSD and ev duration
by Ella Hinton 28 Jul '13

28 Jul '13

Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella

2 1

A question about coordinates
by jh kim 28 Jul '13

28 Jul '13

Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 10000 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates. Are these coordinates in MNI space? Thank you in advance for your answer. Kim

2 2

Combining non accelerated and accelerated MRIs
by Stéphane Poulin 28 Jul '13

28 Jul '13

Dear Freesurfer experts I am using Freesurfer to process part of the ADNI 2 database which includes non accelerated and accelerated images. Images have different voxel sizes. Is there any litterature to guide me what should I do, ie combining or not these scans. Stephane

2 1

FW: VMAC neuroimaging research analyst opening (fwd)
by Bruce Fischl 26 Jul '13

26 Jul '13

FYI From: Jefferson, Angela [mailto:angela.jefferson@Vanderbilt.Edu] Sent: Friday, July 26, 2013 9:36 AM Subject: VMAC neuroimaging research analyst opening Dear colleague, My laboratory at Vanderbilt has a neuroimaging research analyst II opening. If you have students or recent trainees who have 2 years of research experience or a master’s degree equivalent with programming or scientific computing skills who are interested in gaining some research experience in neuroimaging for a couple of years before attending graduate school, this opportunity would be a great fit (especially if they don’t mind relocating to Nashville). If you wouldn’t mind distributing the attached posting to potential candidates, I would very much appreciate it. Best regards, Angela Angela L. Jefferson, PhD Director, Vanderbilt Memory & Alzheimer’s Center Associate Professor of Neurology Vanderbilt University Medical Center 2525 West End Avenue, 12th Floor, Suite 1200 Nashville, TN 37203 www.vanderbiltalzheimers.com www.vanderbiltcognitiveaging.com

1 0

Freesurfer surface circle of pre-defined size
by sarahp＠nmr.mgh.harvard.edu 26 Jul '13

26 Jul '13

Hello Freesurfer Experts, We would like to use PySurfer's function plot_label_foci.py to automatically create circular labels of a pre-defined radius (eg. 14mm) on the fsaverage surface of freesurfer. What are the specified units of "n_steps" in the command line argument "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', n_steps=50"? Thank you, Sarah

2 1

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