Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Jobs: Postdoctoral Fellow - Neuropsychology/Clinical Neuroscience/Imaging
by Emily Rogalski 04 Nov '15

04 Nov '15

http://www.alzforum.org/jobs/postdoctoral-fellow-neuropsychologyclinical-ne… Employer Cleveland Clinic-Lou Ruvo Center for Brain Health Location Las Vegas, Nevada Principal Investigator Please send your CV to Sarah Banks, bankss2(a)ccf.org and Ryan Walsh, walshr(a)ccf.org. Description The Cleveland Clinic Lou Ruvo Center for Brain Health in Las Vegas, Nevada is looking for an outstanding postdoctoral researcher to join the team as soon as possible. The researcher will work with two clinical and translational researchers, Ryan R. Walsh and Sarah Banks, on a recently awarded NIH grant (duration of funds: five years) assessing the neuropsychological and neuroimaging correlates of Alzheimer’s and Parkinson’s diseases. The study utilizes cutting-edge neuroimaging and analytic techniques involving both MRI and PET to assess cross-sectional and longitudinal patterns of cognitive disruption and neuroimaging changes in these patients. As part of the funding mechanism, the researcher will also collaborate with Jeff Cummings, and there is potential for collaboration with another five-year, fully funded project involving multi-modal MRI imaging in Parkinson’s disease, as well as experts in fMRI and PET both at the Cleveland Clinic and other institutions. The Cleveland Clinic Lou Ruvo Center for Brain Health is developing an excellent research team, featuring accessible, affable clinician-scientists in neurology and neuropsychology—a multidisciplinary team, in a small and specialized environment. It has state-of-the-art scanning technology, and a robust neuroimaging core led by Dietmar Cordes, a dedicated MR physicist and his team of research engineers, physicists, and mathematicians. This position will be excellent for anyone who has recently graduated and is looking to rapidly build his or her academic career in a position with no immediate need to obtain external funding. Requirements The ideal candidate will hold a Ph.D. in neuroscience, psychology, or similar field and have an interest in and experience with neurodegenerative disease, cognition, and neuroimaging. He or she will enjoy working in a multidisciplinary team, be productive, and enjoy contributing to every stage of data collection, analysis, and presentation. He or she will hit the ground running, working on existing data sets to answer research questions related to those posed in the grant, and also develop their own projects. Once sufficient data has been accrued from the grant projects, prospective data analysis and manuscript preparation will account for much of the researcher’s time. As such, great communication and writing skills, in addition to statistical knowledge and ability, will be important. -- Emily J Rogalski, PhD Associate Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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preproc-sess and stc question
by Gay,Charles Wysaw 04 Nov '15

04 Nov '15

Hi - 1) I am trying to perform preprocessing steps on functional task data that was acquired on a Phillips scanner using an interleaved acquisition. There are 42 slices and the order is [0,6,12,18,24,30,36,1,7,13,19,25,31,37,2,8,14,20,26,32,38,3,9,15,21,27,33,39,4,10,16,22,28,34,40,5,11,17,23,29,35,41]. I've tried -slice order followed by the sequence but that didn't seem to work. And I wasn't able to find anything in stc-sess -help that explained how to enter the exact sequence order. If you could show me how to add/change the tutorial code below, that would be great. Thanks. 2) Do I need to modify the onsets in the paradigmfile? Thanks, Chaz preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

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Extracing values from ces.nii
by Afzal, Afsana 04 Nov '15

04 Nov '15

Hi, I'm trying to extract the contrast values from ces.nii.gz after first-level analysis. My goal is to average the contrast values for each voxel across subjects for a given condition and see where an individual from a separate population falls within the distribution of contrast values. The ces.nii file I'm working with has the following dimension: (27307, 1, 6, 1), which I interpreted as containing information about 27307 voxels in a 3D matrix. What does the information in the 6 rows for each voxel represent? I was expecting to get a single raw b-value for each voxel. The structure is consistent with sig.nii and t.nii files as well. Thanks for any help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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how to obtain individual's pial_lgi value
by Yang, Daniel 04 Nov '15

04 Nov '15

Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel

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changing the index of labels
by Jacobs H (NP) 04 Nov '15

04 Nov '15

Hi, Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and right, FreeSurfer treats them as different regions? Thanks! Best Heidi > >>I just checked again in freeview and indeed they have the same index >>(e.g. >>CA1 has value 206 for left and also for right). >> >>On 10/27/15, 5:01 PM, "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >> >>>The color is not important. The question is whether they have a >>>different index. Can you confirm that lh and rh have the same index? >>> >>>On 10/27/15 11:53 AM, Jacobs H (NP) wrote: >>>> Hi Doug, >>>> >>>> Yes, for the aseg they are. But not for the hippocampal subfields: >>>>left >>>> and right have the same color coding. >>>> I am creating one segmentation, including left and right hippocampal >>>> subfields and aparc, for partial volume correction. >>>> Any idea how I can make the labels for the hippocampal subfields >>>>different >>>> (freesurfer version 6)? >>>> >>>> Thanks >>>> Heidi >>>> >>>> On 10/27/15, 4:32 PM, "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>wrote: >>>> >>>>> The indices should be different. Eg, 17 is left hippo, 53 is right >>>>> hippo. If you click on them in freeview and different labels appear, >>>>> then FS knows they are different >>>>> >>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote: >>>>>> Hi. >>>>>> >>>>>> Just one another related question: now that I was able to combine >>>>>>left >>>>>> and >>>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed >>>>>> that >>>>>> the left and right hippocampal subfields have the same color labels >>>>>>and >>>>>> codes. What would be the best way to make sure that FreeSurfer >>>>>> understand >>>>>> that the left and right subfields (e.g. Left and right CA1) are >>>>>> different >>>>>> areas? >>>>>> >>>>>> Thanks! >>>>>> Heidi >>>>>> >>>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)" >>>>>> <h.jacobs(a)maastrichtuniversity.nl> >>>>>> wrote: >>>>>> >>>>>>> Thanks! Works wonderful! >>>>>>> Heidi >>>>>>> >>>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve" >>>>>>><greve(a)nmr.mgh.harvard.edu> >>>>>>> wrote: >>>>>>> >>>>>>>> If you want to remove them, you can use mri_binarize with the >>>>>>>> --replace >>>>>>>> option, replacing them with whatever you want. >>>>>>>> >>>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I am trying to generate a segmentation file containing the >>>>>>>>>aseg+aparc >>>>>>>>> but replacing the hippocampus with the hippocampal subfields. >>>>>>>>> With mergeseg I was able to merge the segmentations, but >>>>>>>>> unfortunately >>>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still >>>>>>>>>in >>>>>>>>> there (as the area covered by the subfields is not 100% equal to >>>>>>>>>the >>>>>>>>> hippocampus of the aseg). >>>>>>>>> How can I remove the remains of the old hippocampal labels? >>>>>>>>> >>>>>>>>> Many thanks! >>>>>>>>> Best >>>>>>>>> Heidi >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)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 >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(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. >>>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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 >> >

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Not sure what is going on. can you find (from the log) the command it runs just before that (something with mris_label_calc) and run it in a terminal (with the SUBJECT_DIR set etc). It could be that it get's confused by the .nii extension, but could also be something else. Martin On 11/04/2015 10:09 AM, Heidi Foo wrote: > Hi Martin, > > I understand what you mean now. Thanks for your advice! > > But I have another error message now: /ERROR 64 : mris_label_calc > intersect did not work? /Is there something I am doing wrong? > > Regards, > Heidi > > > On Wed, Nov 4, 2015 at 10:39 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: > > Heidi, > > first: you probably need to keep the .nii in the table for now > (depending on how your cross sectional directories are really > named?). If they have the .nii extension, you need to do the same > in the qdec table. > > If down the road the extension creates problems, it will be very > complicated to solve this as the naming is propagated to many > places (in the cross runs, base and long). Cleaning that up > retrospectively is possible but lot's of work and if you miss a > place things will fail. So it might be easier to re-run from > scratch (depending on the size of the data and the edits)? Let's > first wait and see what happens. > > Best, Martin > > > On 11/04/2015 09:34 AM, Heidi Foo wrote: >> Hi Martin, >> >> Thanks so much for your reply, I really appreciate it. >> >> I will change my qdec file for fsid accordingly from >> FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name >> and file extension are causing the problem, do you have any >> suggestions for me overcome this? Would changing the file name help? >> >> Thanks again. >> >> Regards, >> Heidi >> >> On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter >> <mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >> >> Dear Heidi, >> >> maybe there is a problem with your long.qdec.table.dat file? >> It is used to create the <fsid>.long.<fs_baseid> file names >> and obviously that filename is wrong (containing two .long. >> in it). Make sure that the first column is only the cross >> sectional id and the second one is the base id, so in your case: >> fsid fsid-base >> FS_PD002_1.nii FSBASE_002 >> >> Also it is not a good idea to have the ".nii" as part of the >> subject id, as that is a file extension. Next time, when >> running the cross sectionals, make sure you call the subject >> "FS_PD002_1" without extension. Could be that this leads to >> other problems (or it could just work, we'll see). >> >> Best, Martin >> >> >> >> >> >> On 11/04/2015 08:38 AM, Heidi Foo wrote: >>> Dear FreeSurfer experts, >>> >>> I was running the first stage of analysis of preparing of >>> data - qcache - and I encountered some problems. >>> >>> When 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 --sd $SUBJECTS_DIR/, an >>> error message saying:" >>> FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label >>> does not exist!" appears. >>> >>> I tried several other ways such as using long_stats_slopes, >>> but I keep receiving error messages similar to the one above. >>> >>> Please advice? >>> >>> Thank you so much for your kind help! >>> >>> Regards, >>> Heidi Foo >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >> Web :http://reuter.mit.edu >> >> 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. >> >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> > Web :http://reuter.mit.edu > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 04 Nov '15

04 Nov '15

Hi list, this error is still occurring: mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config fcseed-sess -s -cfg MRS_MASK.config During fcseed-sess -s subj -cfg MRS_MASK.config Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. fcseed-sess.97908/avgwf.mgh Segmentation fault I have read your previous message and you can check the MRS voxel features. MRS voxel mask is in subj directory where I have run recon all -all. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ The features are same of other subject that runs fine. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ Thank you very much. Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 16-ott-2015 23.15 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL > >I'd like to open with FSLview the sig.nii.gz which is produced by >selxavg3-sess. >If I use mri_surf2vol, which is the template to added in --template? >It should be in Tailairach space? Where can I find the template that I >should added? >Thanks, > >Stefano > >subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >data_type FLOAT32 >dim1 27307 >dim2 1 >dim3 6 >dim4 1 >datatype 16 >pixdim1 1.000000 >pixdim2 1.000000 >pixdim3 1.000000 >pixdim4 1100.000000 >cal_max 49.1815 >cal_min -12.3855 >file_type NIFTI-1+ > > > > > > > >Thanks, > >Stefano > > >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 29-set-2015 22.09 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >> >>Do you mean surface-based analysis? You'd have to put them back into >the >>volume using mri_surf2vol, write them out as nifti and then run >fslview >>on them >> >>On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >>> >>> Hi list, >>> >>> I would like to import FS-FAST results (conjunction maps) in >FSL, >>> opening them by fslview. >>> Could you provide me any suggestion? >>> >>> Thank you very much >>> Best regards, >>> >>> >>> Stefano >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 >>Phone Number: 617-724-2358 >>Fax: 617-726-7422 >> >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard. >edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(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. >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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zcat issue, lGI processing
by Andrews, Derek 04 Nov '15

04 Nov '15

Hello Freesurfer Support Team, I have encountered an issue running recon-all -lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this... >> reading filled volume... zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script). Any suggestions or work throughs would be appreciated. Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Heidi, first: you probably need to keep the .nii in the table for now (depending on how your cross sectional directories are really named?). If they have the .nii extension, you need to do the same in the qdec table. If down the road the extension creates problems, it will be very complicated to solve this as the naming is propagated to many places (in the cross runs, base and long). Cleaning that up retrospectively is possible but lot's of work and if you miss a place things will fail. So it might be easier to re-run from scratch (depending on the size of the data and the edits)? Let's first wait and see what happens. Best, Martin On 11/04/2015 09:34 AM, Heidi Foo wrote: > Hi Martin, > > Thanks so much for your reply, I really appreciate it. > > I will change my qdec file for fsid accordingly from > FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name and > file extension are causing the problem, do you have any suggestions > for me overcome this? Would changing the file name help? > > Thanks again. > > Regards, > Heidi > > On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: > > Dear Heidi, > > maybe there is a problem with your long.qdec.table.dat file? It is > used to create the <fsid>.long.<fs_baseid> file names and > obviously that filename is wrong (containing two .long. in it). > Make sure that the first column is only the cross sectional id and > the second one is the base id, so in your case: > fsid fsid-base > FS_PD002_1.nii FSBASE_002 > > Also it is not a good idea to have the ".nii" as part of the > subject id, as that is a file extension. Next time, when running > the cross sectionals, make sure you call the subject "FS_PD002_1" > without extension. Could be that this leads to other problems (or > it could just work, we'll see). > > Best, Martin > > > > > > On 11/04/2015 08:38 AM, Heidi Foo wrote: >> Dear FreeSurfer experts, >> >> I was running the first stage of analysis of preparing of data - >> qcache - and I encountered some problems. >> >> When 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 --sd $SUBJECTS_DIR/, an error message saying:" >> FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label >> does not exist!" appears. >> >> I tried several other ways such as using long_stats_slopes, but I >> keep receiving error messages similar to the one above. >> >> Please advice? >> >> Thank you so much for your kind help! >> >> Regards, >> Heidi Foo > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> > Web :http://reuter.mit.edu > > 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. > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Dear Heidi, maybe there is a problem with your long.qdec.table.dat file? It is used to create the <fsid>.long.<fs_baseid> file names and obviously that filename is wrong (containing two .long. in it). Make sure that the first column is only the cross sectional id and the second one is the base id, so in your case: fsid fsid-base FS_PD002_1.nii FSBASE_002 Also it is not a good idea to have the ".nii" as part of the subject id, as that is a file extension. Next time, when running the cross sectionals, make sure you call the subject "FS_PD002_1" without extension. Could be that this leads to other problems (or it could just work, we'll see). Best, Martin On 11/04/2015 08:38 AM, Heidi Foo wrote: > Dear FreeSurfer experts, > > I was running the first stage of analysis of preparing of data - > qcache - and I encountered some problems. > > When 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 --sd $SUBJECTS_DIR/, an error message saying:" > FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label > does not exist!" appears. > > I tried several other ways such as using long_stats_slopes, but I keep > receiving error messages similar to the one above. > > Please advice? > > Thank you so much for your kind help! > > Regards, > Heidi Foo -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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Freesurfer November 2015