Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Re: [Freesurfer] Dilated PV spaces
by Douglas N Greve 20 Feb '14

20 Feb '14

It is not the dicom file but the rawavg.mgz that is the immediate problem. As for the subject you sent, it is hard to say what is going wrong. It looks like there might be a lot of WM pathology. Is that right? That might be difficult for our intensity normalization. You can try placing control points in voxels that you are sure are WM (and not equal to 110 on the T1.mgz) doug On 02/20/2014 01:06 PM, Victor Kovac wrote: > Hi Doug, > > I will would double-check the dcm files and re-run recon-all on that scan. > > Attached are an image of the segmentation and the recon-all.log file > from another timepoint of this subject. As you can see, a great deal > of cortical gray and white matter is missed. > > Thank you for your help! > Victor > > > On Wed, Feb 19, 2014 at 4:26 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It looks like that file is corrupted. Is this disk full? > > > On 02/19/2014 05:21 PM, Victor Kovac wrote: > > Hi Doug. > > This is the output: > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz... > mghRead(/lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz): > could not read 131072 bytes at slice 150 > > I was wondering if it might be that the dicom file > corresponding to slice 150 was corrupted, so I checked slice > 150 in the sagittal plane, but I see no error. > > Please advise. > > Thanks! > Victor > > > On Wed, Feb 19, 2014 at 3:48 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>>> wrote: > > The log file you sent shows recon-all failing at a very early > point before the issue with the PV spaces could become a > problem. > It appears to fail at this command-line. > > mri_convert > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/orig.mgz > --conform > > Can you run this and post the terminal output to the list > > > > On 02/19/2014 12:08 PM, Victor Kovac wrote: > > Hello FreeSurfer experts, > > > > I have four scans from a subject who has ubiquitous, dilated > > perivascular spaces (image attached) that seem to be > preventing > > recon-all from finishing. I have attached the > recon-all.log from one > > of the scans. > > > > Any advice on what I could try to get these scans > analyzed would be > > greatly appreciated. > > > > Thank you! > > Victor > > > > > > _______________________________________________ > > 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>> > > > 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>> > 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: 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> > > 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>> > > 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 <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: 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/ > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Error in qdec: load data file
by Miranka Wirth 20 Feb '14

20 Feb '14

Hi FreeSurfers, I have trouble loading the .dat file into qdec, receiving the following error message: Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject 'DEM001.freesurfer' in > SUBJECTS_DIR My SUBJECTS_DIR is set correctly and the particular subject exists in this directory. Also, loading one subject works (even though the error message appears) Loading two subjects, is not working. I am thankful for any information what I could check. I have also read earlier comments in the mailing list but could not solve the problem. Cheers Miranka

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running error in mris_preproc
by charujing123 20 Feb '14

20 Feb '14

Hi FS experts, When I ran the mris_preproc, the left hemisphere completely done well, but the right hemisphere exit error.How to fix the error? Thanks. All the best. Here is error back information: --------------------------------------------------- #@# 35/38 PAT_IA29 Thu Feb 20 14:53:26 CST 2014 -------------- ----------------------- mri_surf2surf --srcsubject PAT_IA29 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.29390/PAT_IA29.35.mgh --sval /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/PAT_IA29/surf/rh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = PAT_IA29 srcval = /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/PAT_IA29/surf/rh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.29390/PAT_IA29.35.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/PAT_IA29/surf/rh.sphere.reg Loading source data Reading curvature file /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/PAT_IA29/surf/rh.thickness ERROR: number of vertices in /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/PAT_IA29/surf/rh.thickness does not match surface (148817,148917) ERROR: reading curvature file Reading target surface reg /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (154970) Reverse Loop had 32500 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 138265, nTrgMulti = 25577, MnTrgMultiHits = 2.27067 nSrc121 = 122386, nSrcLost = 0, nSrcMulti = 32584, MnSrcMultiHits = 2.2697 Saving target data Saving to ./tmp.mris_preproc.29393/PAT_IA27.34.mgh Rujng Zha 2014-02-20 charujing123

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Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
by Yang, Daniel 19 Feb '14

19 Feb '14

Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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interaction between two covariates in qdec?
by Yang, Daniel 19 Feb '14

19 Feb '14

Dear FreeSurfer Experts, In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples) it says "Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able." However, I cannot select more than one covariate in qdec. Any suggestion? I'm using qdec in Mac, FreeSurfer 5.3. Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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Re: [Freesurfer] Dilated PV spaces
by Douglas N Greve 19 Feb '14

19 Feb '14

It looks like that file is corrupted. Is this disk full? On 02/19/2014 05:21 PM, Victor Kovac wrote: > Hi Doug. > > This is the output: > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz... > mghRead(/lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz): > could not read 131072 bytes at slice 150 > > I was wondering if it might be that the dicom file corresponding to > slice 150 was corrupted, so I checked slice 150 in the sagittal plane, > but I see no error. > > Please advise. > > Thanks! > Victor > > > On Wed, Feb 19, 2014 at 3:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The log file you sent shows recon-all failing at a very early > point before the issue with the PV spaces could become a problem. > It appears to fail at this command-line. > > mri_convert > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/orig.mgz --conform > > Can you run this and post the terminal output to the list > > > > On 02/19/2014 12:08 PM, Victor Kovac wrote: > > Hello FreeSurfer experts, > > > > I have four scans from a subject who has ubiquitous, dilated > > perivascular spaces (image attached) that seem to be preventing > > recon-all from finishing. I have attached the recon-all.log from one > > of the scans. > > > > Any advice on what I could try to get these scans analyzed would be > > greatly appreciated. > > > > Thank you! > > Victor > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(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. > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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recon-all error on a pediatric case
by Francesco Baldacchini 19 Feb '14

19 Feb '14

I applied recon-all on a pediatric structural image which you can find here https://www.dropbox.com/s/zrfln9psaqffftp/MPRAGE.nii but the process stopped and gave me an error, I attached the .log in this mail. I think the problem is related to the low age of the subject, any hint on to solve this problem or optimize the structural image? Thanks, Francesco Baldacchini

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Error mric-convert
by Saurabh Thakur 19 Feb '14

19 Feb '14

Hello Everyone, I am facing small problem to create my own file //================================// saurabh@saurabh-Precision-WorkStation-T3500:~/Desktop/saurabh_freesurfer/bert/sam$ mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/005.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001... Starting DICOMRead2() dcmfile = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 dcmdir = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam Ref Series No = 501 *Found 156 files, checking for dicoms WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154* Found 151 dicom files in series. WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 First Sorting Computing Slice Direction Vs: -121.791 -125.08 -36.7045 Vs: -0.682698 -0.701136 -0.205747 Second Sorting Counting frames nframes = 1 nslices = 151 *ndcmfiles = 151 MRIalloc(0, 0, 151): bad parmNo such file or directoryERROR: mri alloc failed* //===============================================================// Please reply asap....i m waiting for the solution. Thanks in advanced. cheers Saurabh Thakur,

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Dilated PV spaces
by Victor Kovac 19 Feb '14

19 Feb '14

Hello FreeSurfer experts, I have four scans from a subject who has ubiquitous, dilated perivascular spaces (image attached) that seem to be preventing recon-all from finishing. I have attached the recon-all.log from one of the scans. Any advice on what I could try to get these scans analyzed would be greatly appreciated. Thank you! Victor

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fReadQdec question
by sabin khadka 19 Feb '14

19 Feb '14

Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin

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Freesurfer February 2014