Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

Re: [Freesurfer] proportion of surface area of significant region
by Lars M. Rimol 13 Aug '14

13 Aug '14

Thanks, Doug! So I tried this method using fsaverage/surf/lh.white.avg.area.mgh. The results seem to be reasonably consistent with the ones I get when eyeballing the p-maps overlayed on fsaverage in tksurfer. Would you agree that's a reasonable "sanity check"? When I compare the results to just counting vertices, there doesn't seem to be a huge difference between proportion of #vertices and proportion of surface area. So either there isn't a lot of variance in the sizes of the faces, or the variance is evenly distributed. Finally, if I want to convert from an individual map or the cohort mean map to mm² units, can I do it by scaling the ico area vertex values by the ratio between native and ico total area? So: (vertex value from mean cohort map * total area for cohort mean map) / total area for fsaverage/surf/lh.white.avg.area.mgh, where total area would be the sum of all vertex values? Thank you! LMR ------------------------------------------------------------------------------------------------------- You don't want to get the surface area from the faces of fsaverage. Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug On 07/30/2014 08:38 AM, Lars M. Rimol wrote: > Hi Bruce, > > I would like to be able to tell what proportion of a region of > interest (ROI), as defined in atlas space by e.g. Desikan-Killiany, > that shows a significant effect (based on a p-map). For now I overlay > the p-map on the inflated surface of fsaverage in tksurfer and eyeball > the proportion. > > Given a p-map, if I find the FDR threshold and identify the vertices > within a given ROI that have a p-value greater than the threshold, > then I can find the proportion of the ROI that is suprathreshold. > E.g., I find 1986 suprathreshold vertices in "bankssts" out of 2137, > so 93% of vertices in bankssts show a significant effect. > > My question is: Does that tell me anything about what proportion of > the ROI's surface area is affected in atlas space? Obviously, if the > faces were uniform, there would be a 1 to 1 relationship between > #vertices and area. In the original tesselation of any dataset the > size of the faces is uniform, but that changes with topology fix and > deformation. I assume that is true also for fsaverage? (so I can't > assume [#sig vertices] / [# tot vertices] == the proportion of the > ROI's area that is significant in atlas space) > > I can find the surface area of the suprathreshold region for my sample > (or any subset thereof) by looking at a mean area map. But I'm unsure > how to do that for fsaverage itself? Is there information on regional > surface area directly available? Or would using getFaceArea.m or > getFacesArea.m or similar functions be a solution? > > > Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

2 1

Cortical Segmentation reliability in Mid-Line structures
by amirhossein manzouri 13 Aug '14

13 Aug '14

Dear All, I wonder if you have experienced or there is any report on cortical segmentation reliability in the mid-line structures of the brain, so one should take them into consideration in running group differences with Qdec? Best regards, Amirhossein Manzouri

2 3

V1 and V2 labels valid with clinical populations?
by krista kelly 13 Aug '14

13 Aug '14

Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista

3 5

mri_em_register intervention?
by Makaretz, Sara Johanna 12 Aug '14

12 Aug '14

I am having trouble getting a usable brainmask for one of my subjects - a screenshot of the initial brainmask.mgz is attached as image_1. The talairach transformation looks fine, so I tried running recon-all -multistrip with raised watershed heights to no avail - see image_2. Does this mean the problem is with the mri_em_register step / lta output? How can I check this, and what can I try changing? Thank you!

2 2

Flip ROI in fsaverage / mris_left_right_register
by Bastian Cheng 12 Aug '14

12 Aug '14

Dear Freesurfers, I am trying to flip an overlay (.mgh) to the contralateral hemisphere. The overlay is in fsaverage-space. I am using it only for visualization (and not doing any statistics). I noticed that there was a program that could achieve this: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_left_rig… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_re… However it is not online anymore. Would this still be the right way to do it? Best regards, Bastian

2 2

Mac OS X update
by carolina.mr 12 Aug '14

12 Aug '14

2 1

fsaverage cortex thickness
by wangzhiwei3233 12 Aug '14

12 Aug '14

Hi, all, How to calculate the mean cortex thickness of fsaverage? Thanks! Wilder

3 2

-hippo-subfields
by Gregory Kirk 11 Aug '14

11 Aug '14

we have freesurfer set up on our big condor cluster, i asked that the -hippo-subfields be added. they have it set up to run in 3 stages autorecon1 autorecon2 autorecon3 they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would cause harm, just be ignored in the first 2 ? thanks greg

3 2

Re: [Freesurfer] error loading subjects in QDEC
by McLaughlin, Katie 11 Aug '14

11 Aug '14

Hi Nick et al, Just wanted to follow up on this. It seems as though Nick Schmansky has worked through this issue with previous FS users who have had the same error. We are having an issue with QDEC recognizing subjects in the SUBJECTS_DIR. It is not a permissions issue (777 for all) and all the subjects are in the directory following recon-all and the qcache completed. The data table loads but cannot find any of the subjects. Data table was created in Linux. Nick - we have searched through the archives and haven't found a solution to this issue, although a number of other users have had the same problem. I'm wondering if you've found a solution? Many thanks, Kate Error Output: Reading /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl Using /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42 Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 0.763636 m 0.000000 1.500000 -3.547619 348130.000000 2 1014 c 0.098336 m 0.000000 -11.500000 -10.547619 149370.000000 3 1032 c 2.507636 m 0.000000 2.500000 0.452381 -960.000000 4 1034 c 0.101136 m 0.000000 -15.500000 -11.547619 190570.000000 5 1041 m -2.516264 m 1.000000 17.500000 12.452381 -26620.000000 6 1043 m -1.453964 m 0.000000 7.500000 12.452381 205250.000000 7 1047 c -0.933764 m 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 m 1.171636 f 0.000000 14.500000 7.452381 -42730.000000 9 1077 c 0.281836 f 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 m 0.142136 f 0.000000 3.500000 -1.547619 -158930.000000 11 1096 c -1.711364 f 0.000000 -6.500000 -6.547619 31690.000000 12 1097 c -0.323264 f 0.000000 6.500000 0.452381 -218300.000000 13 1099 c 2.488536 m 0.000000 -14.500000 -8.547619 279160.000000 14 1100 m 1.404336 f 0.000000 9.500000 -0.547619 -77570.000000 15 1114 m -0.312264 f 0.000000 -10.500000 -12.547619 141560.000000 16 1119 m -1.374564 m 0.000000 -7.500000 18.452381 110660.000000 17 1123 m 0.988136 m 0.000000 33.500000 16.452381 -27400.000000 18 1125 c 0.287236 f 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 c -1.820864 m 0.000000 -14.500000 -12.547619 348770.000000 20 1128 c -1.338964 f 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 c -2.086464 f 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 m 1.324936 m 0.000000 12.500000 23.452381 -108080.000000 23 1139 m 0.875936 f 0.000000 -4.500000 0.452381 -199980.000000 24 1142 m -0.851664 f 0.000000 10.500000 2.452381 -386850.000000 25 1143 m -2.820164 f 0.000000 11.500000 -13.547619 -109600.000000 26 1153 m -2.458764 f 0.000000 13.500000 10.452381 369170.000000 27 1154 m -1.234964 f 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 c 1.034736 f 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 m 1.163436 f 0.000000 11.500000 11.452381 -71900.000000 30 1163 m 1.371436 m 0.000000 15.500000 7.452381 239550.000000 31 1165 m -0.517664 m 1.000000 -11.500000 -2.547619 16810.000000 32 1166 m -2.302764 m 1.000000 -7.500000 1.452381 220140.000000 33 1167 m 0.292736 f 1.000000 12.500000 11.452381 -117810.000000 34 1171 c 1.385136 f 0.000000 6.500000 -7.547619 59040.000000 35 1173 c 1.075736 f 0.000000 -7.500000 2.452381 -86380.000000 36 1175 c 1.765736 f 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 c 1.732836 m 0.000000 -11.500000 -3.547619 108560.000000 38 1177 m 0.717136 f 0.000000 -5.500000 10.452381 -53070.000000 39 1178 m -0.241164 f 0.000000 33.500000 15.452381 -110020.000000 40 1179 c 0.944336 f 0.000000 -7.500000 0.452381 15300.000000 41 1180 c 0.760936 f 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 c -0.380764 f 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age_demean continuous 0 3 sex discrete 2 1 m 2 f 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age_demean -0.000 1.410 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248 Number of subjects: 42 Number of factors: 7 (2 discrete, 5 continuous) Number of classes: 4 Number of regressors: 24 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [Katie.McLaughlin(a)childrens.harvard.edu] Sent: Friday, August 01, 2014 5:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC Hi Doug, Same error when data table created in Linux There are a number of messages about this same issue in the Archive (e.g.): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03347… https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h… https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036226… In the second message string, there is some information about bash vs sh in ubuntu potentially generating this error. However, I'm working on a cluster used by a number of others and can't use the fix described by another FS user. I'm wondering if you've resolved this using another strategy previously? Thanks, Kate Error Output: Reading /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl Using /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42 Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 0.763636 m 0.000000 1.500000 -3.547619 348130.000000 2 1014 c 0.098336 m 0.000000 -11.500000 -10.547619 149370.000000 3 1032 c 2.507636 m 0.000000 2.500000 0.452381 -960.000000 4 1034 c 0.101136 m 0.000000 -15.500000 -11.547619 190570.000000 5 1041 m -2.516264 m 1.000000 17.500000 12.452381 -26620.000000 6 1043 m -1.453964 m 0.000000 7.500000 12.452381 205250.000000 7 1047 c -0.933764 m 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 m 1.171636 f 0.000000 14.500000 7.452381 -42730.000000 9 1077 c 0.281836 f 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 m 0.142136 f 0.000000 3.500000 -1.547619 -158930.000000 11 1096 c -1.711364 f 0.000000 -6.500000 -6.547619 31690.000000 12 1097 c -0.323264 f 0.000000 6.500000 0.452381 -218300.000000 13 1099 c 2.488536 m 0.000000 -14.500000 -8.547619 279160.000000 14 1100 m 1.404336 f 0.000000 9.500000 -0.547619 -77570.000000 15 1114 m -0.312264 f 0.000000 -10.500000 -12.547619 141560.000000 16 1119 m -1.374564 m 0.000000 -7.500000 18.452381 110660.000000 17 1123 m 0.988136 m 0.000000 33.500000 16.452381 -27400.000000 18 1125 c 0.287236 f 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 c -1.820864 m 0.000000 -14.500000 -12.547619 348770.000000 20 1128 c -1.338964 f 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 c -2.086464 f 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 m 1.324936 m 0.000000 12.500000 23.452381 -108080.000000 23 1139 m 0.875936 f 0.000000 -4.500000 0.452381 -199980.000000 24 1142 m -0.851664 f 0.000000 10.500000 2.452381 -386850.000000 25 1143 m -2.820164 f 0.000000 11.500000 -13.547619 -109600.000000 26 1153 m -2.458764 f 0.000000 13.500000 10.452381 369170.000000 27 1154 m -1.234964 f 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 c 1.034736 f 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 m 1.163436 f 0.000000 11.500000 11.452381 -71900.000000 30 1163 m 1.371436 m 0.000000 15.500000 7.452381 239550.000000 31 1165 m -0.517664 m 1.000000 -11.500000 -2.547619 16810.000000 32 1166 m -2.302764 m 1.000000 -7.500000 1.452381 220140.000000 33 1167 m 0.292736 f 1.000000 12.500000 11.452381 -117810.000000 34 1171 c 1.385136 f 0.000000 6.500000 -7.547619 59040.000000 35 1173 c 1.075736 f 0.000000 -7.500000 2.452381 -86380.000000 36 1175 c 1.765736 f 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 c 1.732836 m 0.000000 -11.500000 -3.547619 108560.000000 38 1177 m 0.717136 f 0.000000 -5.500000 10.452381 -53070.000000 39 1178 m -0.241164 f 0.000000 33.500000 15.452381 -110020.000000 40 1179 c 0.944336 f 0.000000 -7.500000 0.452381 15300.000000 41 1180 c 0.760936 f 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 c -0.380764 f 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age_demean continuous 0 3 sex discrete 2 1 m 2 f 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age_demean -0.000 1.410 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248 Number of subjects: 42 Number of factors: 7 (2 discrete, 5 continuous) Number of classes: 4 Number of regressors: 24 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 5:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC How did you create your qdec table? It looks like it might have been created on a windows machine. If so, try creating it in linux. doug On 08/01/2014 04:53 PM, McLaughlin, Katie wrote: > Hi Doug, > > The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR (see output below) when loading the data table. > > The subjects are all in the directory, however, with permissions set to 777 on all. I've found a number of previous posts with the same error, but no solution. > > Thanks, > Kate > > > Output from loading data table: > Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... > QdecDataTable::Load: will attempt to open as Mac text file... > Number of columns: 8 > fsid column: 1 > Number of factors: 7 > Number of subjects: 42 > > Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. > Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR > Too many subjects not found! > Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, August 01, 2014 4:09 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM error in QDEC > > So, did it generate the error when you loaded the table or when you hit > analyze? List the steps and buttons that produce this error. > doug > > On 07/31/2014 05:20 PM, McLaughlin, Katie wrote: >> Hi Doug, >> >> I'm using 5.3. >> >> This error was generated when I had more variables in the model, so I used the option within qdec to remove variables from the data table to see if that had any effect (i.e., deleted everything except one categorical variable). Still got the error you see below. >> >> Thanks, >> Kate >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Thursday, July 31, 2014 5:14 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] GLM error in QDEC >> >> What version of FS are you using? When I load that file in 5.3 qdec, it >> creates several discrete classes, see below >> doug >> >> >> 40 1179 c 17.514000 0.944336 f 12.000000 14.000000 0.000000 >> -7.500000 0.452381 1565300.000000 15300.000000 >> 41 1180 c 17.330600 0.760936 f 1.000000 0.000000 0.000000 -18.500000 >> -13.547619 1452200.000000 -97800.000000 >> 42 1181 c 16.188900 -0.380764 f 10.000000 6.000000 0.000000 >> -9.500000 -7.547619 1489390.000000 -60610.000000 >> 1 maltreatment discrete 2 >> 1 c >> 2 m >> 2 age continuous 0 >> 3 age_demean continuous 0 >> 4 sex discrete 2 >> 1 m >> 2 f >> 5 internalizing continuous 0 >> 6 externalizing continuous 0 >> 7 hs_less continuous 0 >> 8 internal_demean continuous 0 >> 9 external_demean continuous 0 >> 10 ICV continuous 0 >> 11 ICV_demean continuous 0 >> Continuous Factors: Mean: StdDev: >> ------------------- ----- ------- >> age 16.570 1.410 >> age_demean -0.000 1.410 >> internalizing 19.500 12.769 >> externalizing 13.548 9.759 >> hs_less 0.119 0.328 >> internal_demean 0.000 12.769 >> external_demean 0.000 9.759 >> ICV 1554609.048 168177.248 >> ICV_demean 4609.048 168177.248 >> >> Number of subjects: 42 >> Number of factors: 11 (2 discrete, 9 continuous) >> Number of classes: 4 >> Number of regressors: 40 >> >> >> >> >> On 07/31/2014 02:27 PM, McLaughlin, Katie wrote: >>> Hi Doug et al, >>> >>> I'm trying to run an analysis in QDEC and continue to get an error >>> that says that the QDEC GLM design creates 0 factors. >>> >>> I'm attaching my data table here as well as the output of QDEC. I've >>> tried deleting all variables in my data file other than one and >>> testing just that comparison, but no luck. >>> >>> Any thoughts are much appreciated. >>> >>> Thanks, >>> Kate >>> >>> SUBJECTS_DIR is >>> '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' >>> Input table: >>> /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat >>> Subj#, SubjID, Data... >>> 1 1009 c >>> 2 1014 c >>> 3 1032 c >>> 4 1034 c >>> 5 1041 m >>> 6 1043 m >>> 7 1047 c >>> 8 1058 m >>> 9 1077 c >>> 10 1094 m >>> 11 1096 c >>> 12 1097 c >>> 13 1099 c >>> 14 1100 m >>> 15 1114 m >>> 16 1119 m >>> 17 1123 m >>> 18 1125 c >>> 19 1126 c >>> 20 1128 c >>> 21 1134 c >>> 22 1137 m >>> 23 1139 m >>> 24 1142 m >>> 25 1143 m >>> 26 1153 m >>> 27 1154 m >>> 28 1157 c >>> 29 1158 m >>> 30 1163 m >>> 31 1165 m >>> 32 1166 m >>> 33 1167 m >>> 34 1171 c >>> 35 1173 c >>> 36 1175 c >>> 37 1176 c >>> 38 1177 m >>> 39 1178 m >>> 40 1179 c >>> 41 1180 c >>> 42 1181 c >>> 1 maltreatment discrete 2 >>> 1 c >>> 2 m >>> Continuous Factors: Mean: StdDev: >>> ------------------- ----- ------- >>> >>> Number of subjects: 42 >>> Number of factors: 1 (1 discrete, 0 continuous) >>> Number of classes: 2 >>> Number of regressors: 2 >>> ============================================================ >>> ERROR: QdecGlmDesign::Create: zero factors! >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> > -- > 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 > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 3

dt_recon error
by Ritobrato Datta 11 Aug '14

11 Aug '14

Hi All, I ran dt_recon and got the following error. Can someone suggest how to fix this ? I have attached the dwi-infodump.dat file for more information. Thanks a lot for the help. Best Rito #@#------------------------------- Fitting Tensors Mon Aug 11 07:29:29 EDT 2014 cd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003 mri_glmfit --y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003 cmdline mri_glmfit --y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat sysname Darwin hostname magi-2-balthasar.uphs.upenn.edu machine x86_64 user iron FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii logyflag 1 X /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat usedti 1 glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon Loading y from /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii Using DTI bValue = 1000 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

2 1

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Freesurfer August 2014