Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

mri_glmfit error
by Marina Fernández 12 May '20

12 May '20

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimental design has less than 12 columns, the analysis is successful. I also send you the fsgd.txt file (through FTP File Exchange). In this file you can see that there are four groups that have been created by the combination of two discrete variables (sex and apoe-type). How can I solve this problem? Thank you in advance. ERROR MESSAGE: (...) Saving design matrix to /usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+08 Design matrix ------------------ 0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.79984 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.84287 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.74935 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.82284 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 0.17882 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.33908 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.71704 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 -0.02652 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 0.46929; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 1.23055; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 -2.38637 0.00000 0.00000 0.00000 -0.90297; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.28399 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.86996 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.18883; 0.00000 1.00000 0.00000 0.00000 0.00000 -2.15871 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 1.53105 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -1.98254 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.73974 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.23391 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.13151 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.91298 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -1.63020 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.78982; 0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000 0.00000 -1.55987 0.00000 0.00000 0.00000 -0.15173 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 1.54087 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 1.28564 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 -0.76775 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.71704 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 1.41085; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.73974; 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 -0.76274 0.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.50731 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 -0.93803 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 0.29975 0.00000 0.00000 0.00000 -1.07325 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 1.74613 0.00000 0.00000 0.00000 -0.46725 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -1.50396 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.65460 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.10169 0.00000 0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 -0.26191 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 0.05361 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 -0.77776 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.22083 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 0.94007 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.74935 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 0.76979 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.71704 0.00000 0.00000 0.00000 -1.76650 0.00000 0.00000 0.00000 -3.43214 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 0.60452; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 0.61954; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -0.22083 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.91503; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 -0.16175 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.27786 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 0.80485 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.21888 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 -0.28194 0.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.22083 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 -0.49229 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.98254 0.00000 0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 0.69968 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 -0.71766 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.55239 0.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -1.10169 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 -2.14502 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 -1.17341 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 2.19214; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 -1.38877 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.08662 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.36470 0.00000 0.00000 0.00000 -1.35325 0.00000 0.00000 0.00000 0.66462 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.36470 0.00000 0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 0.71971 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.58448 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -1.63020 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.95009 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -1.97312 0.00000 0.00000 0.00000 -0.47226 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -1.14662 0.00000 0.00000 0.00000 -0.45222 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 0.12372 0.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 -1.35325 0.00000 0.00000 0.00000 -0.26191 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000 0.00000 0.00000 -1.35325 0.00000 0.00000 0.00000 -0.12168 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 0.39417 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.53737; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 1.10534; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.46429; 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.33908 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.32906 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 -1.55987 0.00000 0.00000 0.00000 -1.73434 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 1.63622; 0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.98310 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 2.36600 0.00000 0.00000 0.00000 -2.40545 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 1.24557 0.00000 0.00000 0.00000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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.bin --surf amy_frapsaliva_average lh --C /usr/local/freesurfer/subjects/amy_frapsaliva_stats/contrast.mat --fsgd /usr/local/freesurfer/subjects/amy_frapsaliva_stats/fsgd.txt dods --label /usr/local/freesurfer/subjects/amy_frapsaliva_average/label/lh.cortex.label --y /usr/local/freesurfer/subjects/amy_frapsaliva_stats/lh.fsgd_subj_gauss001.mgh --no-prune --glmdir /usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.768203 (col 15), Max=6.706254 (col 10) ... could not determine the cause of the problem

1 0

Robust Regression with Univariate LME
by Hua, Jessica 12 May '20

12 May '20

External Email - Use Caution Hi FreeSurfer Experts, There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a robustfit function. Is there a way to modify the lme_fit_FS code to incorporate robust regression? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

1 0

Release 7.0.0 is being recalled, 7.1.0 is ready for download
by Douglas N. Greve 11 May '20

11 May '20

Hi All, I regret to inform you that we are recalling 7.0.0 because we found some small issues with the way that conforming step was being performed. The conforming step takes your input volume and converts it to 256x256x256 1mm and converts the type to UCHAR (8 bit). When converting to UCHAR, it has to do some intensity rescaling. The method for doing this was changed in 7.0.0. In most data sets, this results in small changes to the output. However, we just discovered that it can result in large problems in some data sets, so, for 7.1.0, we are reverting back to the pre-7.0.0 method. Going forward, we recommend that people NOT use 7.0.0 and use 7.1.0 instead. We apologize for any inconvenience this has caused. We hope that not many data sets have been analyzed yet in the 11 days since the release. I'd like to thank our research assistant Devani Cordero for ferreting out this problem. Release notes are here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 7.1.0 can be obtained from here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads Please let us know if you have any problems best doug

1 0

Re: [Freesurfer] Compare individual to a group
by Douglas N. Greve 11 May '20

11 May '20

I guess you could apply your transform to both the healthy controls and to your patient, can then create an FSGD file with two classes as before but no continuous variable. Then just have a contrast that computes the diff between the patient and the mean of the controls. On 5/8/2020 11:49 AM, Xiaojiang Yang wrote: > > External Email - Use Caution > > Hi Douglas, > > Could you please reply my last email (sent to > freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>) regarding my question about > the weighted age? I am eager to listen to your answer/opinion to my > question. For your convenience, I also include the whole email chain > below this email. > > Thank you very much! > > Sincerely, > > Xiao > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > :%22Douglas+N.+Greve%22> Douglas N. Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > :20200507> Thu, 07 May 2020 14:56:08 -0700 > sorry, please include the previous email chain so that I know what you are > referring to > On 5/7/2020 5:33 PM, Xiaojiang Yang wrote: > External Email - Use Caution > Douglas, > Just as I mentioned in the initial email, subjects in the healthy > group have > different ages. Because average cortical thickness is believed to be > declined as the age gets older, I want to "normalize" the group by > multiplying each subject's thickness with an age-dependent scalar > (pre-calculated constant). Suppose I take age 30 as the "standard" > age, then > subjects with ages greater than 30 will have scalars greater than 1 > (depend > on age); subjects with ages smaller than 30 will have scalars less than 1. > In this way, all subjects in the group looks like to be at the same age > (30). > Of course, I also suspect that there is no need to do the above mentioned > normalization if I use mri_glmfit. But my initial intention was using > non-linear scalars, and mri_glmft can only use linear fit. Please give me > your opinion. Thank you! > Xiao > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > :%22Douglas+N.+Greve%22> Douglas N. Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > :20200507> Thu, 07 May 2020 14:06:27 -0700 > I don't know what weight is. Can you elaborate? > On 5/7/2020 4:54 PM, Xiaojiang Yang wrote: > External Email - Use Caution > Hi Douglas, > Thank you very much! Could you please help me with more detailed > information? > 1)Should I use "Variables age" or "Variables age weight" in the fsgd file? > If I can use either of them, which one is better? > I don't know what weight is. Can you elaborate? > 2)For the contrast file, the content "1 -1 0" you mentioned, it > corresponds > to the "Variables age" fsgd file, correct? > Yes > 3)If I use the "Variables age weight" fsgd file, what will be the > content of > the contrast file? Is it "1 -1 0 0"? > Yes > Thank you again! > Xiao > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > :%22Douglas+N.+Greve%22> Douglas N. Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > :20200507> Thu, 07 May 2020 11:55:27 -0700 > I think it will work properly if you use the raw data as input and > create an > FSGD file with two classes: (1) the individual subject and (2) healthy > subjects. Also include age as a covariate. Use DOSS instead of DODS. Then > set your contrast to be 1 -1 0 and run mri_glmfit. I think that should > properly account for age. > On 5/7/2020 2:44 PM, Xiaojiang Yang wrote: > External Email - Use Caution > Dear FS experts, > I have a group of healthy subjects. Given a new individual subject, I want > to compare its cortical thickness to the healthy group so that I can find > where the thickness is abnormal (thickening or thinning). > I use fsaverage as the template subject to calculate mean and std of the > healthy group. Since subjects in the healthy group have different > ages, I do > a "normalization" process to all the subjects in the group BEFORE > calculating the mean and std. Thus the normalized healthy group can be > regarded as all subjects having the same "standard" age. The normalization > process is just multiplying some pre-obtained scale (varied by age, > but not > linearly ) to the file *?h.thickness.fwhm0.fsaverage.mgh* of each subject > that are already calculated by "recon-all --qcache" command. So the > mean and > std of the group are actually weighted in the sense of Freesurfer's > recon-all results. > My questions are: > 1)If I do vertex-wise t-tests by simply comparing individual subject's > thickness to the group using mris_calc but WITHOUT using mri_glmfit, can I > still use mri_glmfit-sim to do multiple comparisons correction? If > yes, how? > 2)If the answer is no for the above question, how should I use > mris_glmft to > implement my above thoughts so that I can use use mri_glmfit-sim? > Specifically, how can I use the weighted mean for the group? > 3)Take a step back, if I consider the weight is linearly correlated > with the > age, how to design the fsdg and contrast file? > Thank you very much! > Xiao >

2 2

(No Subject)
by KennethSPrice 11 May '20

11 May '20

External Email - Use Caution Hello Freesurfer friends! I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --osgm \ --surf fsaverage lh I am getting an ERROR: DOF = 0. MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR. What is the cause of the error? Thanks, Ken Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 5

tkmedit in FreeSurfer 7.0
by Dincer, Aylin 11 May '20

11 May '20

External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: "Tcl_Init returned 1: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4" It looks like when we manually set the environmental variable TCL_LIBRARY to point to the tcl location in the $FREESURFER_HOME folder, tkmedit will open. Is there a way to fix this so it automatically sets this environmental variable? Thanks! Aylin _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Re: [Freesurfer] Hippocampus
by Iglesias Gonzalez, Juan E. 11 May '20

11 May '20

Dera Elisabetta, Can you please give us some more detail on what you mean by “I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes.”? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Del Re, Elisabetta" <Elisabetta_DelRe(a)hms.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, May 11, 2020 at 09:42 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus Dear Freesurfer team, I have analyzed the anterior/posterior hippocampus successfully utilizing FS6.0. I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes. Do you have suggestions? Thank you very much, regards, Elisabetta

3 7

Downloading Matlab runtime - ubuntu
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 11 May '20

11 May '20

External Email - Use Caution Dear Freesurfer experts, I'm trying to download runtime for ubuntu using the instructions on the website and I'm struggling to resolve this error (seen below). Any ideas on how to fix this? Thank you and hope everyone is safe! cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_inst… -o fs_install_mcr && chmod +x fs_install_mcr % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file fs_install_mcr: Permission denied 68 1988 68 1371 0 0 4436 0 --:--:-- --:--:-- --:--:-- 4422 curl: (23) Failed writing body (0 != 1371) alex@ubu19:/usr/local/freesurfer/bin$ fs_install_mcr R2012b % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 177 100 177 0 0 77 0 0:00:02 0:00:02 --:--:-- 77 Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period. Thank you, Alex Job Said

3 3

Get Atlas surfaces in subject space
by Ian 11 May '20

11 May '20

External Email - Use Caution Hi Freesurfers. I have a subject S with recon-all having been run on it. I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white, and rh.white. I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject space. Any helpers on how to achieve this? Thanks, Ian -- *Ian Hardingham*

5 29

Re: [Freesurfer] Recon-all exited WITH errors
by Mason Wells 11 May '20

11 May '20

External Email - Use Caution Hi Doug, Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what’s going on or how to fix it? Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 20:01 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} External Email - Use Caution Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz... reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial... reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white... reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1698 1132 3274 2.730 0.526 0.130 0.032 26 2.4 caudalanteriorcingulate 4375 2908 8369 2.594 0.599 0.127 0.040 46 7.0 caudalmiddlefrontal 3883 2464 5378 2.087 0.498 0.149 0.082 74 9.4 cuneus 546 373 1423 2.817 0.999 0.154 0.087 11 1.9 entorhinal 5411 3506 10979 2.768 0.567 0.137 0.059 101 14.8 fusiform 6159 4159 11629 2.543 0.520 0.133 0.045 86 11.0 inferiorparietal 5973 3945 13736 2.965 0.705 0.138 0.060 130 13.4 inferiortemporal 1536 934 2788 2.725 0.838 0.164 0.090 50 5.1 isthmuscingulate 6953 4476 11030 2.320 0.542 0.147 0.055 110 15.3 lateraloccipital 3897 2512 7780 2.641 0.630 0.147 0.077 99 13.1 lateralorbitofrontal 5273 3237 7567 2.161 0.603 0.151 0.956 191 20.8 lingual 2015 1290 4210 2.576 0.773 0.157 0.084 64 6.5 medialorbitofrontal 6073 4091 14456 3.026 0.553 0.130 0.043 80 11.0 middletemporal 1012 711 2254 2.886 0.735 0.133 0.112 16 6.3 parahippocampal 2182 1401 4296 2.690 0.669 0.128 0.044 26 4.5 paracentral 3247 2175 6722 2.682 0.501 0.121 0.038 34 5.1 parsopercularis 1195 793 2520 2.549 0.514 0.138 0.045 21 2.1 parsorbitalis 2780 1882 5377 2.457 0.608 0.131 0.043 37 5.0 parstriangularis 2229 1444 2359 1.685 0.476 0.155 0.067 41 6.1 pericalcarine 7692 4818 11728 2.218 0.657 0.130 0.053 114 16.0 postcentral 1983 1360 4109 2.902 0.617 0.167 0.079 44 6.1 posteriorcingulate 7681 4765 13220 2.521 0.549 0.123 0.056 119 15.1 precentral 6240 4189 11573 2.532 0.576 0.145 0.052 104 13.3 precuneus 1613 992 3166 2.820 0.661 0.136 0.055 54 3.6 rostralanteriorcingulate 6644 4495 12118 2.347 0.579 0.144 0.052 117 13.9 rostralmiddlefrontal 12967 8768 28469 2.839 0.612 0.132 0.047 170 25.1 superiorfrontal 7963 5213 12201 2.095 0.481 0.125 0.053 125 16.2 superiorparietal 9021 6069 20753 3.059 0.612 0.130 0.050 183 19.9 superiortemporal 7970 5269 15543 2.684 0.502 0.149 0.074 910 17.4 supramarginal 702 454 1432 2.844 0.618 0.133 0.046 8 1.3 transversetemporal 2953 1947 6539 3.228 0.801 0.124 0.056 33 6.4 insula Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 19:56 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed} Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly? On 5/4/2020 2:49 PM, Mason Wells wrote: External Email - Use Caution Hi, Terminal output is below: /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz... mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 From: <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 4 May 2020 at 18:54 To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited WITH errors Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white On 5/4/2020 1:34 PM, Mason Wells wrote: External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…>

2 7

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer