Re: [Freesurfer] Longitudinal analysis of rates or percent changes
Hi Martin, Thanks for your reply. I removed the time column from the qdec table (below is some sample content of the new qdec table): fsid fsid-base age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 76 y AD F x x x x m24 Then I re-ran with —generic-time long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --generic-time --stack-rate ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt This produced difference in all results (for stacked rate, pc1/fit, and spc). Can we now conclude that if the time column is present in the qdec table, the --generic-time flag does not have any influence to the results and the results are calculated using the specified time value and not the values 1,2,3,4 for the time points (regardless the --generic-time flag in the command)? Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: Monday, February 13, 2017 7:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Katarina, sorry, did not see your previous mail until now. In the future, if you put "longitudinal” somewhere in the subject line, chances are higher that I find it (but not guaranteed either :-) I think using the real time vs using -generic time should give different results in the SPC. Subject slopes should differ depending on this change in x-axis (which is the time axis, and y is the thickness/volume). So something seems wrong. I wonder if the generic time is not working? Maybe it get’s overwritten by the time column in your file. I used it in the past, in cases where there is no time column, if I remember that correctly. You can try to remove the time column and re-run with —generic time to see if that produces a difference. Best, Martin On 10 Feb 2017, at 13:36, Katarina Trojacanec mailto:katarina.trojaca...@finki.ukim.mk>> wrote: Hi Freesurfer team, I am sorry for writing again. Would you please be able to answer my last question? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Katarina Trojacanec mailto:katarina.trojaca...@finki.ukim.mk>> Sent: Friday, February 3, 2017 9:02 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Fw: Analysis of rates or percent changes This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing<http://aka.ms/LearnAboutSpoofing> Feedback<http://aka.ms/SafetyTipsFeedback> Hi Martin, Apologies for multiple e-mails, but I got a message that something might be wrong with the previous e-mail, so I forward it again. Please find below my previous question. Regards, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ____ From: Katarina Trojacanec Sent: Thursday, February 2, 2017 2:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, I dropped --generic-time flag as you suggested in the previous e-mail and run the long_stats_slopes command again like this: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt However, I got exactly the same results for stacked rate pc1/fit, spc (the files long_AD_NL_TP1_2_
Re: [Freesurfer] Fw: Analysis of rates or percent changes
Hi Freesurfer team, I am sorry for writing again. Would you please be able to answer my last question? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Katarina Trojacanec Sent: Friday, February 3, 2017 9:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fw: Analysis of rates or percent changes This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing<http://aka.ms/LearnAboutSpoofing> Feedback<http://aka.ms/SafetyTipsFeedback> Hi Martin, Apologies for multiple e-mails, but I got a message that something might be wrong with the previous e-mail, so I forward it again. Please find below my previous question. Regards, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ____ From: Katarina Trojacanec Sent: Thursday, February 2, 2017 2:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, I dropped --generic-time flag as you suggested in the previous e-mail and run the long_stats_slopes command again like this: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt However, I got exactly the same results for stacked rate pc1/fit, spc (the files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the --generic-time flag. Is this reasonable? As I read and understood, the --generic-time flag assumes that time difference between the time points is 1, which is not true in my case (the time difference between TP1 and TP2 is around six months, and between TP2 and TP3, as well as TP3 and TP4 is one year). This indicates that there should be some difference in the result. Am I doing something wrong or misunderstood anything, or maybe there are some temporary files from the first running of the command that are used also in the second one (without --generic-time flag)? Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ____ From: Katarina Trojacanec Sent: Monday, September 12, 2016 10:01:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, Thanks a lot. Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: Monday, September 12, 2016 7:58:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Katarina, different time spacing is OK (not optimal, but OK). This 2-stage procedure first fits a line in each subject, independent on how many time points the subject has. Of course a linear fit from 4 time points will be more reliable than one from just 2 time points. This is not taken into consideration and therefore we usually recommend the Linear Mixed Effects modeling (where it is considered in the model). If most of your subjects have 4 time points and the spacing is similar (across subjects) you should be fine. Other things I noticed: - you should drop the --generic-time flag. I probably should change the help text to be more specific, but what it does it assigns a time of 1 2 3 4 to the time points (this is if you do repeated measures and there is no real time). So don't pass it. - you can drop some of the --do... flags. Probably you are interested in the rate and one of the pct change flags. The average is just the average thickness (across time) for each subject. Not sure you want to analyze that. The --do-stack is a subject-specific stack of the time points, usually only used for debugging. - the -stack-avg is not needed unless you want to analyze average thickness for each subject, rather you may want to create a stack for the rate or the pc1 or whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or whatever you use). Best, Martin On 09/12/2016 12:40 PM, Katarina Trojacanec wrote: Hi, I have a question abou
[Freesurfer] Fw: Analysis of rates or percent changes
Hi Martin, Apologies for multiple e-mails, but I got a message that something might be wrong with the previous e-mail, so I forward it again. Please find below my previous question. Regards, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: Katarina Trojacanec Sent: Thursday, February 2, 2017 2:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, I dropped --generic-time flag as you suggested in the previous e-mail and run the long_stats_slopes command again like this: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt However, I got exactly the same results for stacked rate pc1/fit, spc (the files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the --generic-time flag. Is this reasonable? As I read and understood, the --generic-time flag assumes that time difference between the time points is 1, which is not true in my case (the time difference between TP1 and TP2 is around six months, and between TP2 and TP3, as well as TP3 and TP4 is one year). This indicates that there should be some difference in the result. Am I doing something wrong or misunderstood anything, or maybe there are some temporary files from the first running of the command that are used also in the second one (without --generic-time flag)? Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: Katarina Trojacanec Sent: Monday, September 12, 2016 10:01:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, Thanks a lot. Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: Monday, September 12, 2016 7:58:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Katarina, different time spacing is OK (not optimal, but OK). This 2-stage procedure first fits a line in each subject, independent on how many time points the subject has. Of course a linear fit from 4 time points will be more reliable than one from just 2 time points. This is not taken into consideration and therefore we usually recommend the Linear Mixed Effects modeling (where it is considered in the model). If most of your subjects have 4 time points and the spacing is similar (across subjects) you should be fine. Other things I noticed: - you should drop the --generic-time flag. I probably should change the help text to be more specific, but what it does it assigns a time of 1 2 3 4 to the time points (this is if you do repeated measures and there is no real time). So don't pass it. - you can drop some of the --do... flags. Probably you are interested in the rate and one of the pct change flags. The average is just the average thickness (across time) for each subject. Not sure you want to analyze that. The --do-stack is a subject-specific stack of the time points, usually only used for debugging. - the -stack-avg is not needed unless you want to analyze average thickness for each subject, rather you may want to create a stack for the rate or the pc1 or whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or whatever you use). Best, Martin On 09/12/2016 12:40 PM, Katarina Trojacanec wrote: Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x
Re: [Freesurfer] Analysis of rates or percent changes
Hi Martin, I dropped --generic-time flag as you suggested in the previous e-mail and run the long_stats_slopes command again like this: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc ./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt However, I got exactly the same results for stacked rate pc1/fit, spc (the files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the --generic-time flag. Is this reasonable? As I read and understood, the --generic-time flag assumes that time difference between the time points is 1, which is not true in my case (the time difference between TP1 and TP2 is around six months, and between TP2 and TP3, as well as TP3 and TP4 is one year). This indicates that there should be some difference in the result. Am I doing something wrong or misunderstood anything, or maybe there are some temporary files from the first running of the command that are used also in the second one (without --generic-time flag)? Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: Katarina Trojacanec Sent: Monday, September 12, 2016 10:01:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Martin, Thanks a lot. Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: Monday, September 12, 2016 7:58:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Katarina, different time spacing is OK (not optimal, but OK). This 2-stage procedure first fits a line in each subject, independent on how many time points the subject has. Of course a linear fit from 4 time points will be more reliable than one from just 2 time points. This is not taken into consideration and therefore we usually recommend the Linear Mixed Effects modeling (where it is considered in the model). If most of your subjects have 4 time points and the spacing is similar (across subjects) you should be fine. Other things I noticed: - you should drop the --generic-time flag. I probably should change the help text to be more specific, but what it does it assigns a time of 1 2 3 4 to the time points (this is if you do repeated measures and there is no real time). So don't pass it. - you can drop some of the --do... flags. Probably you are interested in the rate and one of the pct change flags. The average is just the average thickness (across time) for each subject. Not sure you want to analyze that. The --do-stack is a subject-specific stack of the time points, usually only used for debugging. - the -stack-avg is not needed unless you want to analyze average thickness for each subject, rather you may want to create a stack for the rate or the pc1 or whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or whatever you use). Best, Martin On 09/12/2016 12:40 PM, Katarina Trojacanec wrote: Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approxim
Re: [Freesurfer] Analysis of rates or percent changes
Hi Martin, Thanks a lot. Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: Monday, September 12, 2016 7:58:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analysis of rates or percent changes Hi Katarina, different time spacing is OK (not optimal, but OK). This 2-stage procedure first fits a line in each subject, independent on how many time points the subject has. Of course a linear fit from 4 time points will be more reliable than one from just 2 time points. This is not taken into consideration and therefore we usually recommend the Linear Mixed Effects modeling (where it is considered in the model). If most of your subjects have 4 time points and the spacing is similar (across subjects) you should be fine. Other things I noticed: - you should drop the --generic-time flag. I probably should change the help text to be more specific, but what it does it assigns a time of 1 2 3 4 to the time points (this is if you do repeated measures and there is no real time). So don't pass it. - you can drop some of the --do... flags. Probably you are interested in the rate and one of the pct change flags. The average is just the average thickness (across time) for each subject. Not sure you want to analyze that. The --do-stack is a subject-specific stack of the time points, usually only used for debugging. - the -stack-avg is not needed unless you want to analyze average thickness for each subject, rather you may want to create a stack for the rate or the pc1 or whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or whatever you use). Best, Martin On 09/12/2016 12:40 PM, Katarina Trojacanec wrote: Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approximately 6 months and TP3 and TP4 are separated approximately 12 months, are the annualized percent change or atrophy rates using this scenario reasonable (statistically?). Is it maybe more reasonable to apply the same scenario using three time points (for example TP1, TP3 and TP4 from the previous example and the template based only on these time points with the same approximate difference between all of them of 12 months, or TP1, TP2 and TP3 from the previous example and the template based only on these time points with the same approximate difference between all of them of 6 months)? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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 HelpL
[Freesurfer] Analysis of rates or percent changes
Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approximately 6 months and TP3 and TP4 are separated approximately 12 months, are the annualized percent change or atrophy rates using this scenario reasonable (statistically?). Is it maybe more reasonable to apply the same scenario using three time points (for example TP1, TP3 and TP4 from the previous example and the template based only on these time points with the same approximate difference between all of them of 12 months, or TP1, TP2 and TP3 from the previous example and the template based only on these time points with the same approximate difference between all of them of 6 months)? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ___ 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] Correcting defect
Hi Bruce, I already double checked and it looks like all time points are from the same subject. Please find attached the processing commands I used step-by-step (the same I sent you in the previous mail about this question). Do you need some more detailed information? Cheers. Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Saturday, May 7, 2016 4:03:28 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect Hi Katarina how did you create the orig.mgz for these subjects? Either some registration failed badly or you tried to average data from different subjects (see attached tiffs of the orig.mgz you uploaded) cheers Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Hi Bruce, > > I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the > cross-sectionally processed time points for TP1, TP2, and TP4). In the > meantime, one of them, template TP1_4 has finished with error. The other one > (base TP2_4) is still running. > > What do you suggest in this situation. > > Sorry for the inconvenience. > > Cheers. > > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Thursday, May 5, 2016 4:20:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > Hi Katarina > > if you want us to look you need to upload the entire subject dirs (tarred > and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D > mode and just see what the big defects look like. If you load the > orig.nofix at the same time you can goto a vertex in the big defect you see > on the inflated by typing its index into the info winwo for the orig.nofix. > This will be automated in v6 > > Bruce > > > On Thu, 5 May 2016, Katarina Trojacanec wrote: > >> Thank you. >> I have uploaded the files (lh.inflated_TP_1_4.nofix and >> lh.inflated_TP_2_4.nofix). >> >> What should I do as a next step? >> >> Cheers >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Bruce Fischl >> >> Sent: Wednesday, May 4, 2016 2:35 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Correcting defect >> >> sure. Or you can load the ?h.inflated.nofix and look at it - it should be >> obvious if there is a huge defect (you can also load the file >> ?h.defect_labels as an overlay on that surface and it will show you the >> segmentation of the defects) >> >> cheers >> Bruce >> On Wed, 4 May 2016, Katarina Trojacanec wrote: >> >>> >>> Dear FreeSurfer Team, >>> >>> >>> I have been trying to run creation of template with FreeSurfer. However, >>> for two cases for one patient (case 1: template based on TP1 and TP4, case >>> 2: template based on TP2 and TP4), the correcting defect step is running >>> too long. According to the information in the mail archive, the defects are >>> probably too big, and that is the reason for the long processing. >>> >>> >>> May I send you via ftp the subjects directories so you can help me to >>> proceed with this subject, because I am not able to figure out and correct >>> the problem? Should I send you the base directories in their current state >>> or the cross-sectionally processed time points as well? >>> >>> >>> Best Regards, >>> >>> >>> Katarina Trojacanec, M.Sc. >>> Teaching and research assistant >>> >>> Faculty of Computer Science and Engineering >>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@n
Re: [Freesurfer] correcting defects
Yes, it is a longitudinal analysis. I'm waiting for Martin's reply. Thanks for your time. cheers Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Saturday, May 7, 2016 4:12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] correcting defects so this is a longitudinal analysis then? If they are really the same subject, which I'm still not sure about as I think there were big differences in ventricle size (although it's hard to be sure just looking at the average) then there was a dramatic failure of registration. Martin: which volumes would you want to confirm this one way or the other? cheers Bruce On Sat, 7 May 2016, Katarina Trojacanec wrote: > Hi Bruce, > > I checked and it looks like all time points are from the same subject. The > first lines of the recon-all.log confirm that. Please find attached the > processing commands I used step-by-step. > > cheers > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Saturday, May 7, 2016 4:18:52 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] correcting defects > > Hi Katarina > > how did you create the orig.mgz for these subjects? Either some registration > failed badly or you tried to average data from different subjects (see > attached > tiff of one of the orig.mgz you uploaded) > > cheers > Bruce > On Thu, 5 May 2016, Katarina Trojacanec wrote: > >> Hi Bruce, >> >> I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the >> cross-sectionally processed time points for TP1, TP2, and TP4). In the >> meantime, one of them, template TP1_4 has finished with error. The other one >> (base TP2_4) is still running. >> >> What do you suggest in this situation. >> >> Sorry for the inconvenience. >> >> Cheers. >> >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Bruce Fischl >> >> Sent: Thursday, May 5, 2016 4:20:31 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Correcting defect >> >> Hi Katarina >> >> if you want us to look you need to upload the entire subject dirs (tarred >> and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D >> mode and just see what the big defects look like. If you load the >> orig.nofix at the same time you can goto a vertex in the big defect you see >> on the inflated by typing its index into the info winwo for the orig.nofix. >> This will be automated in v6 >> >> Bruce >> >> >> On Thu, 5 May 2016, Katarina Trojacanec wrote: >> >>> Thank you. >>> I have uploaded the files (lh.inflated_TP_1_4.nofix and >>> lh.inflated_TP_2_4.nofix). >>> >>> What should I do as a next step? >>> >>> Cheers >>> Katarina Trojacanec, M.Sc. >>> Teaching and research assistant >>> >>> Faculty of Computer Science and Engineering >>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >>> >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Bruce Fischl >>> >>> Sent: Wednesday, May 4, 2016 2:35 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Correcting defect >>> >>> sure. Or you can load the ?h.inflated.nofix and look at it - it should be >>> obvious if there is a huge defect (you can also load the file >>> ?h.defect_labels as an overlay on that surface and it will show you the >>> segmentation of the defects) >>> >>> cheers >>> Bruce >>> On Wed, 4 May 2016, Katarina Trojacanec wrote: >>> >>>> >>>> Dear FreeSurfer Team, >>>> >>>> >>>> I have been trying to run creation of template with FreeSurfer. However, >>>&
Re: [Freesurfer] correcting defects
Hi Bruce, I checked and it looks like all time points are from the same subject. The first lines of the recon-all.log confirm that. Please find attached the processing commands I used step-by-step. cheers Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Saturday, May 7, 2016 4:18:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] correcting defects Hi Katarina how did you create the orig.mgz for these subjects? Either some registration failed badly or you tried to average data from different subjects (see attached tiff of one of the orig.mgz you uploaded) cheers Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Hi Bruce, > > I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the > cross-sectionally processed time points for TP1, TP2, and TP4). In the > meantime, one of them, template TP1_4 has finished with error. The other one > (base TP2_4) is still running. > > What do you suggest in this situation. > > Sorry for the inconvenience. > > Cheers. > > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Thursday, May 5, 2016 4:20:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > Hi Katarina > > if you want us to look you need to upload the entire subject dirs (tarred > and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D > mode and just see what the big defects look like. If you load the > orig.nofix at the same time you can goto a vertex in the big defect you see > on the inflated by typing its index into the info winwo for the orig.nofix. > This will be automated in v6 > > Bruce > > > On Thu, 5 May 2016, Katarina Trojacanec wrote: > >> Thank you. >> I have uploaded the files (lh.inflated_TP_1_4.nofix and >> lh.inflated_TP_2_4.nofix). >> >> What should I do as a next step? >> >> Cheers >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Bruce Fischl >> >> Sent: Wednesday, May 4, 2016 2:35 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Correcting defect >> >> sure. Or you can load the ?h.inflated.nofix and look at it - it should be >> obvious if there is a huge defect (you can also load the file >> ?h.defect_labels as an overlay on that surface and it will show you the >> segmentation of the defects) >> >> cheers >> Bruce >> On Wed, 4 May 2016, Katarina Trojacanec wrote: >> >>> >>> Dear FreeSurfer Team, >>> >>> >>> I have been trying to run creation of template with FreeSurfer. However, >>> for two cases for one patient (case 1: template based on TP1 and TP4, case >>> 2: template based on TP2 and TP4), the correcting defect step is running >>> too long. According to the information in the mail archive, the defects are >>> probably too big, and that is the reason for the long processing. >>> >>> >>> May I send you via ftp the subjects directories so you can help me to >>> proceed with this subject, because I am not able to figure out and correct >>> the problem? Should I send you the base directories in their current state >>> or the cross-sectionally processed time points as well? >>> >>> >>> Best Regards, >>> >>> >>> Katarina Trojacanec, M.Sc. >>> Teaching and research assistant >>> >>> Faculty of Computer Science and Engineering >>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >>> >>> >> ___ >> 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
Re: [Freesurfer] Correcting defect
Hi Bruce, I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the cross-sectionally processed time points for TP1, TP2, and TP4). In the meantime, one of them, template TP1_4 has finished with error. The other one (base TP2_4) is still running. What do you suggest in this situation. Sorry for the inconvenience. Cheers. Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Thursday, May 5, 2016 4:20:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect Hi Katarina if you want us to look you need to upload the entire subject dirs (tarred and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D mode and just see what the big defects look like. If you load the orig.nofix at the same time you can goto a vertex in the big defect you see on the inflated by typing its index into the info winwo for the orig.nofix. This will be automated in v6 Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Thank you. > I have uploaded the files (lh.inflated_TP_1_4.nofix and > lh.inflated_TP_2_4.nofix). > > What should I do as a next step? > > Cheers > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Wednesday, May 4, 2016 2:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > sure. Or you can load the ?h.inflated.nofix and look at it - it should be > obvious if there is a huge defect (you can also load the file > ?h.defect_labels as an overlay on that surface and it will show you the > segmentation of the defects) > > cheers > Bruce > On Wed, 4 May 2016, Katarina Trojacanec wrote: > >> >> Dear FreeSurfer Team, >> >> >> I have been trying to run creation of template with FreeSurfer. However, >> for two cases for one patient (case 1: template based on TP1 and TP4, case >> 2: template based on TP2 and TP4), the correcting defect step is running >> too long. According to the information in the mail archive, the defects are >> probably too big, and that is the reason for the long processing. >> >> >> May I send you via ftp the subjects directories so you can help me to >> proceed with this subject, because I am not able to figure out and correct >> the problem? Should I send you the base directories in their current state >> or the cross-sectionally processed time points as well? >> >> >> Best Regards, >> >> >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> > ___ > 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
Re: [Freesurfer] Correcting defect
Thank you. I have uploaded the files (lh.inflated_TP_1_4.nofix and lh.inflated_TP_2_4.nofix). What should I do as a next step? Cheers Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Wednesday, May 4, 2016 2:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect sure. Or you can load the ?h.inflated.nofix and look at it - it should be obvious if there is a huge defect (you can also load the file ?h.defect_labels as an overlay on that surface and it will show you the segmentation of the defects) cheers Bruce On Wed, 4 May 2016, Katarina Trojacanec wrote: > > Dear FreeSurfer Team, > > > I have been trying to run creation of template with FreeSurfer. However, > for two cases for one patient (case 1: template based on TP1 and TP4, case > 2: template based on TP2 and TP4), the correcting defect step is running > too long. According to the information in the mail archive, the defects are > probably too big, and that is the reason for the long processing. > > > May I send you via ftp the subjects directories so you can help me to > proceed with this subject, because I am not able to figure out and correct > the problem? Should I send you the base directories in their current state > or the cross-sectionally processed time points as well? > > > Best Regards, > > > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > ___ 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] Correcting defect
Dear FreeSurfer Team, I have been trying to run creation of template with FreeSurfer. However, for two cases for one patient (case 1: template based on TP1 and TP4, case 2: template based on TP2 and TP4), the correcting defect step is running too long. According to the information in the mail archive, the defects are probably too big, and that is the reason for the long processing. May I send you via ftp the subjects directories so you can help me to proceed with this subject, because I am not able to figure out and correct the problem? Should I send you the base directories in their current state or the cross-sectionally processed time points as well? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ___ 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] niiRead error
Dear experts, After running recon-all I got this output: --- Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 x86_64 GNU/Linux /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD mri_convert /home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz mri_convert /home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz INFO: using NIfTI-1 qform niiRead(): error reading from /home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii... ERROR: Read 70, expected 256 Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon Aug 31 13:10:05 CEST 2015 For more details, see the log file /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer -rw-rw-r-- 1 katarina.trojachanec margi 17946 Aug 31 13:10 /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 x86_64 GNU/Linux # #@# MotionCor Mon Aug 31 13:10:10 CEST 2015 ERROR: no run data found in /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri. Make sure to have a volume called 001.mgz in /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon Aug 31 13:10:10 CEST 2015 For more details, see the log file /home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- This is happening only for one file (from multiple that I have tried with). Would you please be able to answer me what might be the problem? Thank you in advance. Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia ___ 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.
