[Freesurfer] Checking optseq efficiency of a custom par file.
Dear Freesurfer list, Using the optseq2 program, is it possible to calculate the efficiency of a custom par file? I have an fMRI task that will be split into three blocks. I want to calculate the overall efficiency of my overall design byconcatenating the best par file from optimizing each individual block. I have already tried doing so by concatenating the three par files (updating the onset times) and inputting this into optseq2 by: >> optseq2 --in new_file.par --nosearch --tr 1.75 --ntp 1080 --psdwin 0 3.5 1.75 --o new_dir If I do this, however, I get a "core dump" error. Does anyone know how I might going about doing this? I've attached the new_par file for convenience. Best, sam new_file.par Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_label2annot & CLUT error
Instead of using an echo this time, I inputted the direct paths straight into the command line. I am in the tcsh shell. On Thu, Sep 10, 2015 at 10:25 AM, Bruce Fischl wrote: > did you try putting an echo in front to see how it expands? What shell are > you using? > > On Thu, 10 Sep 2015, Sam Zorowitz wrote: > > Hi Bruce, >> Thank you for the reply. I had been running it through python. After >> running the command from the >> command line, however, I am still receiving the same error. >> >> Best, >> Sam >> >> On Thu, Sep 10, 2015 at 9:00 AM, Bruce Fischl >> wrote: >> Hi Sam >> >> are you running this from a unix/linux command line? The >> usually >> means >> matlab. In any case, it looks like $CTAB is not being expanded by >> the >> shell. Try using echo to see what the actual command is. >> >> cheers >> Bruce >> >> >> On Thu, 10 Sep 2015, >> Sam Zorowitz wrote: >> >> > Hi all, >> > >> > I am trying to make a custom annotation file. In doing so, I have >> created a custom color >> lookup table. >> > I have attached the CLUT. I run the following command: >> > >> > >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a >> $OUT --l label_1 --l >> label_2 ... --l >> > label_n >> > >> > And I receive the following error: >> > >> > >> CTABreadASCII($CTAB): badly formed file >> > >> Reading ctab $CTAB >> > >> ERROR: reading $CTAB >> > >> > I have searched the archives for similar problems. The only >> previous hit I could find is >> someone who >> > had made the CLUT on Windows -- but I have made mine on Unix and >> the character encoding >> is us-ascii. >> > >> > Any advice from the listserv? Thanks! >> > >> > -Sam >> > >> > >> ___ >> Freesurfer mailing list >> 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. >> >> >> >> > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] mris_label2annot & CLUT error
Hi Bruce, Thank you for the reply. I had been running it through python. After running the command from the command line, however, I am still receiving the same error. Best, Sam On Thu, Sep 10, 2015 at 9:00 AM, Bruce Fischl wrote: > Hi Sam > > are you running this from a unix/linux command line? The >> usually means > matlab. In any case, it looks like $CTAB is not being expanded by the > shell. Try using echo to see what the actual command is. > > cheers > Bruce > > > On Thu, 10 Sep 2015, > Sam Zorowitz wrote: > > > Hi all, > > > > I am trying to make a custom annotation file. In doing so, I have > created a custom color lookup table. > > I have attached the CLUT. I run the following command: > > > > >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a $OUT > --l label_1 --l label_2 ... --l > > label_n > > > > And I receive the following error: > > > > >> CTABreadASCII($CTAB): badly formed file > > >> Reading ctab $CTAB > > >> ERROR: reading $CTAB > > > > I have searched the archives for similar problems. The only previous hit > I could find is someone who > > had made the CLUT on Windows -- but I have made mine on Unix and the > character encoding is us-ascii. > > > > Any advice from the listserv? Thanks! > > > > -Sam > > > > > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list 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.
[Freesurfer] mris_label2annot & CLUT error
Hi all, I am trying to make a custom annotation file. In doing so, I have created a custom color lookup table. I have attached the CLUT. I run the following command: >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a $OUT --l label_1 --l label_2 ... --l label_n And I receive the following error: >> CTABreadASCII($CTAB): badly formed file >> Reading ctab $CTAB >> ERROR: reading $CTAB I have searched the archives for similar problems. The only previous hit I could find is someone who had made the CLUT on Windows -- but I have made mine on Unix and the character encoding is us-ascii. Any advice from the listserv? Thanks! -Sam #$Id: Lausanne250LUT.txt v 1.00 2015/09/08 $ #No. Label Name: R G B A 0 unknown 0 0 0 0 1 bankssts_1 65 67 128 2 bankssts_2 64 68 128 3 bankssts_3 64 67 129 4 caudalanteriorcingulate_1 129 75 64 5 caudalanteriorcingulate_2 128 76 64 6 caudalmiddlefrontal_1 94 128 64 7 caudalmiddlefrontal_2 93 129 64 8 caudalmiddlefrontal_3 93 128 65 9 caudalmiddlefrontal_4 95 128 64 10 caudalmiddlefrontal_5 93 130 64 11 caudalmiddlefrontal_6 93 128 66 12 corpuscallosum 94 64 128 13 cuneus_1 129 86 64 14 cuneus_2 128 87 64 15 cuneus_3 128 86 65 16 entorhinal_1 65 128 67 17 frontalpole_1 65 111 128 18 fusiform_1 83 128 64 19 fusiform_2 82 129 64 20 fusiform_3 82 128 65 21 fusiform_4 84 128 64 22 fusiform_5 82 130 64 23 fusiform_6 82 128 66 24 fusiform_7 85 128 64 25 fusiform_8 82 131 64 26 inferiorparietal_1 129 64 118 27 inferiorparietal_10 128 65 118 28 inferiorparietal_2 128 64 119 29 inferiorparietal_3 130 64 118 30 inferiorparietal_4 128 66 118 31 inferiorparietal_5 128 64 120 32 inferiorparietal_6 131 64 118 33 inferiorparietal_7 128 67 118 34 inferiorparietal_8 128 64 121 35 inferiorparietal_9 132 64 118 36 inferiortemporal_1 65 122 128 37 inferiortemporal_2 64 123 128 38 inferiortemporal_3 64 122 129 39 inferiortemporal_4 66 122 128 40 inferiortemporal_5 64 124 128 41 inferiortemporal_6 64 122 130 42 inferiortemporal_7 67 122 128 43 inferiortemporal_8 64 125 128 44 insula_1 65 128 122 45 insula_2 64 129 122 46 insula_3 64 128 123 47 insula_4 66 128 122 48 insula_5 64 130 122 49 insula_6 64 128 124 50 insula_7 67 128 122 51 isthmuscingulate_1 129 118 64 52 isthmuscingulate_2 128 119 64 53 isthmuscingulate_3 128 118 65 54 lateraloccipital_1 65 78 128 55 lateraloccipital_10 64 79 128 56 lateraloccipital_11 64 78 129 57 lateraloccipital_2 66 78 128 58 lateraloccipital_3 64 80 128 59 lateraloccipital_4 64 78 130 60 lateraloccipital_5 67 78 128 61 lateraloccipital_6 64 81 128 62 lateraloccipital_7 64 78 131 63 lateraloccipital_8 68 78 128 64 lateraloccipital_9 64 82 128 65 lateralorbitofrontal_1 129 64 86 66 lateralorbitofrontal_2 128 65 86 67 lateralorbitofrontal_3 128 64 87 68 lateralorbitofrontal_4 130 64 86 69 lateralorbitofrontal_5 128 66 86 70 lateralorbitofrontal_6 128 64 88 71 lateralorbitofrontal_7 131 64 86 72 lingual_1 116 64 128 73 lingual_2 115 65 128 74 lingual_3 115 64 129 75 lingual_4 117 64 128 76 lingual_5 115 66 128 77 lingual_6 115 64 130 78 lingual_7 118 64 128 79 lingual_8 115 67 128 80 medialorbitofrontal_1 65 89 128 81 medialorbitofrontal_2 64 90 128 82 medialorbitofrontal_3 64 89 129 83 medialorbitofrontal_4 66 89 128 84 medialorbitofrontal_5 64 91 128 85 middletemporal_1 65 128 100 86 middletemporal_2 64 129 100 87 middletemporal_3 64 128 101 88 middletemporal_4 66 128 100 89 middletemporal_5 64 130 100 90 middletemporal_6 64 128 102 91 middletemporal_7 67 128 100 92 paracentral_1 72 64 128 93 paracentral_2 71 65 128 94 paracentral_3 71 64 129 95 paracentral_4 73 64 128 96 paracentral_5 71 66 128 97 parahippocampal_1 129 107 64 98 parahippocampal_2 128 108 64 99 parahippocampal_3 128 107 65 100 parsopercularis_1 127 64 128 101 parsopercularis_2 126 65 128 102 parsopercularis_3 126 64 129 103 parsopercularis_4 128 64 128 104 parsorbitalis_1 83 64 128 105 parsorbitalis_2 82 65 128 106 parstriangularis_1 72 128 64 107 parstriangularis_2 71 129 64 108 parstriangularis_3 71 128 65 109 pericalcarine_1 116 128 64 110 pericalcarine_2 115 129 64 111 pericalcarine_3 115 128 65 112 postcentral_1 65 128 78 113 postcentral_10 64 129 78 114 postcentral_11 64 128 79 115 postcentral_12 66 128 78 116 postcentral_13 64 130 78 117 postcentral_14 64 128 80 118 postcentral_2 67 128 78 119 postcentral_3 64 131 78 120 postcentral_4 64 128 81 121 postcentral_5 68 128 78 122 postcentral_6 64 132 78 123 postcentral_7 64 128 82 124 postcentral_8 69 128 78 125 postcentral_9 64 133 78 126 posteriorcingulate_1 65 100 128 127 posteriorcingulate_2 64 101 128 128 posteriorcingulate_3 64 100 129 129 posteriorcingulate_4 66 100 128 130 precentral_1 129 64 107 131 precentral_10 128 65 107 132 precentral_11 128 64 108 133 precentral_12 130 64 107 134 precentral_13 128 66 107 135 precentral_14 128 64 109 136 precentral_15 131 64 107 137 precentral_16 128 67 107 138 precentral_2 128 64 110 139 precentral_3 132 64 107 140 precentral_4 128 68 107 141 precentral_5 128 64 111 142 precentral_6 133 6
[Freesurfer] mri_watershed mask and skull surfaces
Hi all, I am using mri_watershed to create skull surfaces for a cohort of subjects for whom we were unable to collect a FLASH sequence. To improve the estimation of the inner skull layer, I would like to use edited brainmasks. However whenever I supply the -mask flag, and only when I supply -mask flag to mri_watershed, the code does not run; it only brings up the help screen. So two questions: (1) Is the -mask flag in mri_watershed doing what I think it is doing? Is it masking the T1 image to only the brain so that the inner skull layer will be estimated from the brainmask? (2) Am I using the -mask flag correctly? I get the same result if I use mri_watershed -mask and mri_watershed -mask . Should I be doing something differently? All the best, Sam ___ Freesurfer mailing list 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.
[Freesurfer] mri_watershed problems
Dear Freesurfer community, I am running into issues with mri_watershed, which I am using the create the BEM surfaces. In testing different preflooding height threshold (recommended for accurate skull-stripping), I am running into the issues that an -h 56 produces results where the cerebellum is stripped away, but -h 57 leaves far too much non-brain material in the image. As a result, my BEM surfaces are unrepresentative of the brain (either shrunken in or enlarged). I do, however, already have a satisfying brain-mask. Is there a way to pass the brain mask to mri_watershed to create new BEM surfaces without it creating a new brain mask? Sam Zorowitz Clinical Research Coordinator Division of Neurotherapeutics Department of Psychiatry: Neurosciences Massachusetts General Hospital 149 13th Street, Rm 2620e Charlestown, MA 02129 ___ Freesurfer mailing list 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.
