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30088 discussions

recon-all -s exited with ERRORS
by Carolina Valencia 13 Jun '11

13 Jun '11

Hello Freesurfer's users, I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all, I type: recon-all –i 001.mgz –subject hptu_subj001 –all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> recon-all –i 001.mgz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i 001.mgz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 then I tried with: cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i MPRAGE.nii.gz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 How I can fix this error? Thanks a lot, Best regards, Carolina

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Tracula question: trac-all config file and number of B0 specification
by Deryk S. Beal, Ph.D. 13 Jun '11

13 Jun '11

Dear Tracula Users Does Tracula assume that the number of B0 scans, specified in Step 7.3 of the config file tutorial (below), are the first X number of volumes in the 4Dnii.gz file or will the Tracula routines know from the bvals file where the B0 scans are ordered in the file? For example, I have two runs of 16 directions + 2 B0s each for each of my subjects. I have merged the two runs together and the resulting file has the volumes ordered such that the bvals are entered into Tracula as follows: 0 0 1000 1000 1000 etc 0 0 1000 1000 1000 etc My question pertains to the following part of the Tracula config file: *Step7.3: Specifying Number Of low-b Images* The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* Thank you in advance for your help. Cheers, Deryk Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO Speech-Language Pathologist C.I.H.R. Post Doctoral Research Fellow Department of Cognitive and Neural Systems Speech Laboratory Boston University, 677 Beacon Street, Boston, MA 02215 dsbeal(a)bu.edu http://blogs.bu.edu/dsbeal/about/ ************************************************************************* This email may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. Opinions, conclusions or other information expressed or contained in this email are not given or endorsed by the sender unless otherwise affirmed independently by the sender.

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Re: [Freesurfer] Whole brain parcellation.
by Douglas N Greve 13 Jun '11

13 Jun '11

Anything that is non-0 will cover the whole brain. doug Sudhin A. Shah wrote: > Hi, thank you. Is there a range in the labels that will ensure that I am including the whole brain? I.e. I see labels for Cx, but not subcortical.. > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain? > > Thank you, > S > > > > On Jun 13, 2011, at 10:59 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > >> That is fine, or you can use mri_binarize with the --match option. The numbers that correspond to each label can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as I described in my previous email with tkmedit: >> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg >> >> doug >> >> >> Sudhin A. Shah wrote: >> >>> I mean that I am using FSL to create binary masks from freesurfer parcellated regions. Unless there is a better way :) >>> >>> S >>> >>> >>> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> >>>> What do you mean you are doing it with FEAT? >>>> >>>> Sudhin A. Shah wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. >>>>> >>>>> I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. >>>>> >>>>> Thank you, >>>>> >>>>> S >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> 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 >> >> > > > -- 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

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qustions about contents of label file
by ZhiLiangLong 13 Jun '11

13 Jun '11

Hello: I use qdec to generate statistical significant areas and draw ROI and map the ROI to each subject ,finally i get a label file of each subject called lh.supriorfrontal.label which can be seen in attachment below.But i'm a little confused with content of the label file, Is it correct that,take the third row as an example,the first number 66847 means vertex index and -10.184 -3.059 74.153 means coordinate which belongs to MNI coordinate system? Besides,what does the last number 0.000000 mean? Any help will be appreciative,Thanks

2 1

A question about the coords of the vertex
by soft.join Huang 13 Jun '11

13 Jun '11

Hi all, I have a question about the coords of vertex in ?h.white file. I load the ?h.white file in Matlab and get a variable called vertex_coords, and I'm wondering what kind of coords they are, MNI or something else? Also how can I get the MNI coords of the vertex? Thank in advance, Best Regards, Lijie Huang

2 1

make_average_subject error in T1.mgz and t1.mgz
by tulu＠ms36.hinet.net 13 Jun '11

13 Jun '11

Dear FS experts, I use FS5.1 and previous data run on other machine. When I try to make_average_subjects program, I get error message that it can not get T1.mgz data from subject folder. When I check my dataset, actually it has t1.mgz rather than T1.mgz. how could I change the setting from T1.mgz to t1.mgz thanks help JLH

3 2

aseg labels 96 and 97
by Andrew Ward 13 Jun '11

13 Jun '11

Hi FS experts, We have some legacy code (in a BASH script) that uses mri_cor2label to convert what it is calling the anterior amygdala to volumetric labels. However, we get the error that these values (96 and 97) do not exist. Have the label IDs changed? We are using stable5.1. Our call looks like this: mri_cor2label --c ${FSDIR}/${SUBJID}/mri/aseg.mgz --id 96 --l ${FSDIR}/ ${SUBJID}/label2/lh.amygdala_ant_vol.label Does anyone know what is going on with this? Thank you for your help, Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Rm 2689C Charlestown, MA 02129 Phone: 617-726-6211 Fax: 617-726-5760

2 1

interpretation of qdec results
by tulu＠ms36.hinet.net 13 Jun '11

13 Jun '11

Dear FS experts, I use qdec to do two group study. in QDEC, it set Normal = 1 and Disease = 2, use&nbsp;AGE as covariate&nbsp;and apply DODS model, after analyze group cortical thickness, it showed significant negative T value (blue color) in some brain areas. I have two questions in qdec 1. the contrast&nbsp; set as 1 -1 0 0 but I don't know if it represents as Normal - Disease (normal group is thinner than Disease) or Disease - Normal (disease group is thinner than normal) ? 2. is this results come from correction of multiple comparison ? or I still need to re-set FDR level (default is 0.05) and re-run it ? thanks in advance JLH

1 0

Whole brain parcellation.
by Sudhin A. Shah 10 Jun '11

10 Jun '11

Hello, I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. Thank you, S

2 1

MEMPR and longitudinal processing stream
by Thomas, Adam (NIH/NIMH) [E] 10 Jun '11

10 Jun '11

When using MEMPR images (Van der Kouwe et al., 2008) in the longitudinal processing stream, when should the dura correction (mris_makes_surfaces -dura) be ran? After the first cross-sectional run of recon-all, after the final longitudinal run of recon-all, or maybe both? I have the same question with respect to the "-hippo-subfields" flag. Should this flag be specified on each run of recon-all in the longitudinal processing stream? Thanks, -Adam

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