Re: [Freesurfer] QDEC failed due to missing files
Thank you Doug! Manish From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2015 8:58 AM Subject: Re: [Freesurfer] QDEC failed due to missing files You need to run recon-all -s subject -qcache doug On 04/21/2015 06:34 PM, Manish Dalwani wrote: > Hello Freesurfers, > > In the past I have been able to run QDEC v 4.5 on images without any > problem. Recently I ran recon-all on some new set of images. I was > able to run the regression analyses using command line options. > However, when I tried running qdec..it failed and I get the following > message: > > "Couldn't open > /Applications/freesurfer/subjects/anat_5020/surf/lh.thickness.fwhm10.fsaverage.mgz > > or .mgh file." > > For some reason, the subjects lacked all the smoothed file of 0,5, 10, > etc. in the surf folder. What do you think is the problem? > > Kindly advise! > > Regards, > Manish Dalwani > Instructor > Dept. of Psychiatry > Univ. of CO > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] QDEC failed due to missing files
Hello Freesurfers, In the past I have been able to run QDEC v 4.5 on images without any problem. Recently I ran recon-all on some new set of images. I was able to run the regression analyses using command line options. However, when I tried running qdec..it failed and I get the following message: "Couldn't open /Applications/freesurfer/subjects/anat_5020/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." For some reason, the subjects lacked all the smoothed file of 0,5, 10, etc. in the surf folder. What do you think is the problem? Kindly advise! Regards,Manish DalwaniInstructorDept. of PsychiatryUniv. of CO ___ 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] Can QDEC do a vertex-wise GM comparison?
I am sorry I meant gray matter comparison. Is QDEC GUI toolbox ready at this point to do a vertex-wise gray matter comparison? Sent from my iPhone On Jan 28, 2014, at 5:33 PM, Douglas N Greve wrote: > > > Do you mean having a different model at each vertex (like the --pvr > option for mri_glmfit)? No, sorry > doug > > On 01/28/2014 07:21 PM, Manish Dalwani wrote: >> Dear Freesurfer developers, >> >> Is QDEC GUI toolbox ready at this point to do a vertex-wise GM comparison? >> >> Regards >> Manish Dalwani >> Instructor >> Dept. of Psychiatry >> Univ. of Co >> >> Sent from my iPhon >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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@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
[Freesurfer] Can QDEC do a vertex-wise GM comparison?
Dear Freesurfer developers, Is QDEC GUI toolbox ready at this point to do a vertex-wise GM comparison? Regards Manish Dalwani Instructor Dept. of Psychiatry Univ. of Co Sent from my iPhon ___ 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] Help with QDEC error
Hello again, I also tried the command line options. I get an error for ill-conditioned matrix. Could it be because of possible correlations between covariates? For example I am using Age and mean thickness, should I just use one of them? Here is the error: wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mlh.thickness.CD.10.mgh lh.thickness.CD.10.mris_preproc.log wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir gdfReadHeader: reading FSGD_CD.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 16.6492 1.13124 1 Meanthickness 2.4772 0.0616129 2 IQ 98.08 8.24097 3 CD 6.44 2.77244 Class Means of each Continuous Variable 1 PATIENTS 16.6492 2.4772 98.0800 6.4400 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir sysname Darwin hostname wrls-guest-166-198.ucdenver.edu machine i386 user manishdalwani FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh logyflag 0 usedti 0 FSGD FSGD_CD.fsgd labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness_CD.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness_CD.glmdir Loading y from /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.thickness_CD.glmdir/Xg.dat Normalized matrix condition is 22815.1 Design matrix -- 1.000 15.320 2.500 104.000 2.000; 1.000 18.250 2.440 113.000 9.000; 1.000 18.080 2.460 108.000 3.000; 1.000 14.600 2.560 96.000 11.000; 1.000 14.350 2.580 109.000 6.000; 1.000 17.620 2.530 90.000 6.000; 1.000 16.990 2.500 102.000 7.000; 1.000 17.720 2.450 96.000 6.000; 1.000 17.170 2.450 99.000 7.000; 1.000 17.100 2.360 92.000 1.000; 1.000 16.010 2.460 83.000 4.000; 1.000 17.040 2.430 95.000 4.000; 1.000 17.730 2.490 104.000 2.000; 1.000 15.280 2.480 100.000 8.000; 1.000 16.440 2.390 105.000 10.000; 1.000 16.700 2.580 95.000 8.000; 1.000 16.840 2.460 93.000 9.000; 1.000 17.710 2.380 115.000 5.000; 1.000 15.120 2.470 86.000 11.000; 1.000 16.780 2.520 99.000 7.000; 1.000 15.100 2.420 86.000 5.000; 1.000 16.060 2.510 88.000 6.000; 1.000 18.490 2.430 92.000 7.000; 1.000 16.700 2.610 102.000 11.000; 1.000 17.030 2.470 100.000 6.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 22815.1 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir 2. The FSGD file (if using one) 3. And the design matrix above From: Manish Dalwani To: Douglas Greve Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, June 24, 2013 1:01 PM Subject: Re: [Freesurfer] Help with QDEC error Hi Nick and Doug, Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments. Best, Manish From: Douglas Greve To: Manish Dalwani Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, > > >I realized that I hadn't updated my group levels to one group. However, when I >do that..the qdec complains about group.level having at minimum two levels. >How can I run (using QDEC) single group regression? > > >Thanks, >Manish > > > > > From: Manish Dalwani >To: Douglas Greve ; >"freesurfer@nmr.mgh.harvard.edu" >
Re: [Freesurfer] Help with QDEC error
Hi Nick and Doug, Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments. Best, Manish From: Douglas Greve To: Manish Dalwani Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, > > >I realized that I hadn't updated my group levels to one group. However, when I >do that..the qdec complains about group.level having at minimum two levels. >How can I run (using QDEC) single group regression? > > >Thanks, >Manish > > > >____ > From: Manish Dalwani >To: Douglas Greve ; >"freesurfer@nmr.mgh.harvard.edu" >Sent: Thursday, June 20, 2013 1:26 PM >Subject: Re: [Freesurfer] Help with QDEC error > > > >Hi Doug, > > >I was out of town for a conference. Please see my attachments. I have the log >file and screenshots of ill-matrix conditioning. >Thanks for your help! >Manish > > > > > From: Douglas Greve >To: freesurfer@nmr.mgh.harvard.edu >Sent: Saturday, June 15, 2013 11:09 AM >Subject: Re: [Freesurfer] Help with QDEC error > > > > >Can you send the mri_glmfit.log file from >/Applications/freesurfer/subjects/qdec/Untitled ? >doug > > > >On 6/14/13 4:57 PM, Manish Dalwani wrote: > >Hello Freesurfers, >> >> >>I am trying to run regression analyses within patients and one variable of >>interest which adjusting for the nuisance variables age, IQ, thickness. When >>i select the group and the CD (variable of interest) and run analyses (DODS), >>I get the following error: >> >> >>Qdec 1.4 (Qdec1.4) >> >> >>Type: Error >>Time: Fri Jun 14 14:49:37 2013 >>Description: Error in Analyze: command failed: mri_glmfit --y >>/Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd >>/Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir >>/Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >> --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat >> --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat >> --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat >> >> >>Please advice! >> >> >>Regards, >>Manish Dalwani >>Instructor >>Dept. of Psychiatry >>University of Colorado >> >> >>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >___ >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] Help with QDEC error
Hi Doug and Freesurfers, I realized that I hadn't updated my group levels to one group. However, when I do that..the qdec complains about group.level having at minimum two levels. How can I run (using QDEC) single group regression? Thanks, Manish From: Manish Dalwani To: Douglas Greve ; "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 1:26 PM Subject: Re: [Freesurfer] Help with QDEC error Hi Doug, I was out of town for a conference. Please see my attachments. I have the log file and screenshots of ill-matrix conditioning. Thanks for your help! Manish From: Douglas Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, June 15, 2013 11:09 AM Subject: Re: [Freesurfer] Help with QDEC error Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, > > >I am trying to run regression analyses within patients and one variable of >interest which adjusting for the nuisance variables age, IQ, thickness. When i >select the group and the CD (variable of interest) and run analyses (DODS), I >get the following error: > > >Qdec 1.4 (Qdec1.4) > > >Type: Error >Time: Fri Jun 14 14:49:37 2013 >Description: Error in Analyze: command failed: mri_glmfit --y >/Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd >/Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir >/Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat > --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat > --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat > > >Please advice! > > >Regards, >Manish Dalwani >Instructor >Dept. of Psychiatry >University of Colorado > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] Help with QDEC error
Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado___ 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] Freesurfer error..recon-all fails
Sorry for the bunch of emails. I registered and got the license file. I have been using this software after a long time and feel silly that this was the thing that was causing trouble. Thank you Doug! Manish From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: > Hello Freesurfer's > > I am working on the MAC OS 10.8 and just recently installed the > freesurfer on this server machine. > > I have checked the permissions to various and folders and they look ok > to me. > > When I run the following command: > recon-all -i MR100021.dcm -s test2 > > I get the following error > server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > Actual FREESURFER_HOME /Applications/freesurfer > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/test2 > \n mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n > mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz > -- > ERROR: FreeSurfer license file /Applications/freesurfer/license.txt > not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -- > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > > recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 > > For more details, see the log file > /Applications/freesurfer/subjects/test2/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > I am attaching the log file as well, and would appreciate if people > can help with this issue. > > Best Regards, > Manish Dalwani > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] Freesurfer error..recon-all fails
Ok I checked the other version of freesurfer and I do have .license file in the freesurfer folder. How can I get this file? Best, Manish From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: > Hello Freesurfer's > > I am working on the MAC OS 10.8 and just recently installed the > freesurfer on this server machine. > > I have checked the permissions to various and folders and they look ok > to me. > > When I run the following command: > recon-all -i MR100021.dcm -s test2 > > I get the following error > server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > Actual FREESURFER_HOME /Applications/freesurfer > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/test2 > \n mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n > mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz > -- > ERROR: FreeSurfer license file /Applications/freesurfer/license.txt > not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -- > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > > recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 > > For more details, see the log file > /Applications/freesurfer/subjects/test2/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > I am attaching the log file as well, and would appreciate if people > can help with this issue. > > Best Regards, > Manish Dalwani > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] Freesurfer error..recon-all fails
yes, there is a file called LICENSE in the freesurfer folder. Should I look for something else? Thanks, Manish From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 4, 2013 10:15 AM Subject: Re: [Freesurfer] Freesurfer error..recon-all fails Does the license fileexist? Note it is not called license.txt On 06/04/2013 12:13 PM, Manish Dalwani wrote: > Hello Freesurfer's > > I am working on the MAC OS 10.8 and just recently installed the > freesurfer on this server machine. > > I have checked the permissions to various and folders and they look ok > to me. > > When I run the following command: > recon-all -i MR100021.dcm -s test2 > > I get the following error > server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > Actual FREESURFER_HOME /Applications/freesurfer > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/test2 > \n mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n > mri_convert > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm > /Applications/freesurfer/subjects/test2/mri/orig/001.mgz > -- > ERROR: FreeSurfer license file /Applications/freesurfer/license.txt > not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -- > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... > Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue > Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 > > recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 > > For more details, see the log file > /Applications/freesurfer/subjects/test2/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > I am attaching the log file as well, and would appreciate if people > can help with this issue. > > Best Regards, > Manish Dalwani > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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. LICENSE 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.
[Freesurfer] Freesurfer error..recon-all fails
Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR100021.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani recon-all.log 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.
[Freesurfer] SORRY POSTED THE WRONG ERROR..This is the the right one
I need help with this error...I do see the a LICENSE file in the freesurfer directory. -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s 5214 exited with ERRORS at Mon Jun 3 16:24:01 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/5214/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] help with this error
Dear Freesurfer's I have been using (a slightly older version) Freesurfer on linux and it works fine. I just recently installed freesurfer on the mac workstation OS X 10.8.1. I get the following error: server:subjects manishdalwani$ cd anat_5214 server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s 5214 ERROR: MR100021.dcm exists but is not readable Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Mon Jun 3 15:57:24 MDT 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Kindly help! Regards, Manish___ 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.
