Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Display FSL PALM(permutation) stats in freeview
by Ajay Kurani 20 Sep '16

20 Sep '16

Hello Freesurfer Experts, I was running permutation simulations on cortical thickness data and I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I then tried FSL's PALM which is an extension of randomize to calculate threshold free stats. I saved the output as logp(which is similar to qdec I believe), however I have not been able to load the stats files correctly. The output of palm is lh.thickness_tfce.mgz for my various contrasts. 1) Is .mgz the proper format for the stats files or do I need to convert this to another type like .mgh etc? 2) Can I display this in freeview or is another program needed? I also tried tksurfer but when I loaded the stats file as an overlay nothing displayed. I want to make sure that the stats is loaded as an overlay in freeview/tksurfer and if so, do I need to select anything special so that it scales the logp values correctly? Thanks, Ajay

2 6

mris_calc cluster infos
by Nick Corriveau Lecavalier 19 Sep '16

19 Sep '16

Hi Freesurfer team, I have a 2 Group (MCI, CTL) x 2 (Time1, Time2) protocol. As suggested in an earlier discussion, I measured the rate atrophy for each group between my two time points. Then I applied the clusterwise correction for multiple comparison, which give a lot of information about each group (for example, number of clusters, # of voxels, regions where there's a significant difference). Then I used mris_calc to compute the difference between my groups. My question is: Is there a way to obtain the same informations on the group difference? Since mris_calc doesn't have a .log as output, I can't compute mris_glmfit-sim on it and I cannot get any infos on the cluster summary. Regards, Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

2 1

Anatomy File Orientation Question
by Sepeta, Leigh 19 Sep '16

19 Sep '16

Hi all, I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip) and then looked at the brainmask and mprage in SPM and they both seem to be oriented correctly (left is left, right is right for each one--using anatomical landmarks as the guide). However, in reading up on this topic, many people advise using commands like these (often with RAS) when converting mgz to nii: mri_convert --in_type mgz --out_type nii --out_orientation RAS brainmask.mgz brainmask.nii.gz OR mri_convert --out_orientation RAS -rt nearest --reslice_like <reference.nii or reference.nii.gz> <input.mgz> <output.nii> OR mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary when going between mgz/nii for freesurfer to spm analyses if you know that the mgz and nii files are in the same orientation? Thank you, Leigh <mailto:lsepeta@childrensnational.org> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

1 0

FoV in additional scan
by Vaz pandolfo, Renata 19 Sep '16

19 Sep '16

Dear Eugenio, We have another question about the Hippo Sf Segmentation with an additional scan. Some of our additional scans (FLAIRs or T2s) have a bigger field of view as compared to the T1 (ex.: they cover more of the neck almost up to the shoulders of the subjects, while the T1 has the "normal" FoV). Should the additional scan be cropped or preprocessed in any way (ex.: bias field correction)? And if so, should we process the T1 in the same way or is it generally recommended to just use the raw images? Thank you! Renata

3 4

FLAIR for hippo subfield segmentation with an additional scan
by Vaz pandolfo, Renata 19 Sep '16

19 Sep '16

Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID> Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use? Thank you, Renata

5 8

make_average_volume problems
by Claudia Dacquino 19 Sep '16

19 Sep '16

Hi all, I'm trying making average volume from a set of subjects after making average-subject, but I get this error line: mghWrite(/home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1/.mgh, -1): could not open file And then: Applying LTAtransformInterp (resample_type 1) writing to /home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1.mgh... ERROR: failure writing /home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1/.mgh /home/Admin/Scrivania/SUBJ ERROR: mri_convert failed. I'm quite sure my partition is not full and I have permissions. Any ideas? Thanks a lot. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

1 0

Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 19 Sep '16

19 Sep '16

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging and fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a four-month online theoretical module (starting on October 17th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez, Joaquim Radua and Raymond Salvador FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

1 0

Unpacking DWI Data
by Emily Louise Belleau 18 Sep '16

18 Sep '16

Hello Freesurfer Experts, Our research team has recently collected data from Martinos Center. The entire scanning protocol (including anatomical, functional runs, DWI) is in one directory. Therefore I have been using unpacksdcmdir to tell me what runs go with each scanning sequence. I have had no trouble unpacking the functional and anatomical runs. I have had difficulties unpacking the DWI data. I have been recently warned that unpackdcmdir does not correctly unpack DWI data. Is there a work around or another tool I could use? It seems that most tools are for unpacking per run (dcmtonii), and would not work in my situation where all scans are in one folder? The runs that say "err" which typically indicated something is missing in the scan appear to be unpacking. However, it does say on the terminal that there is an error but attempting to unpack anyway. Some of the runs that say "ok" in the scan log are not unpacking properly. Additionally, we are finding that when we unpack on of the DWI sequences we used, we get bvec and bval files. However, we do not when we unpack a different DWI sequence we also ran we do not get the corresponding bvec and bval files. The command I am using, where I put related runs into related folders: unpacksdcmdir -src dicomdir -targ targetdir -fsfast \ -run 2 bold nii f.nii \ -run 3 bold nii f.nii \ -run 4 bold nii f.nii \ -run 5 bold nii f.nii \ -run 6 bold nii f.nii \ -run 8 3danat mgz 001.mgz \ -run 9 3danat mgz 001.mgz Any help would be great appreciated! Thanks! Rmily

2 4

optseq2 downloading pb
by Alexandre Obert 18 Sep '16

18 Sep '16

Dear all, I would like to download optseq2 from https://surfer.nmr.mgh.harvard.edu/optseq/ it remains unavailable for several days. Is there any other way to obtain it ? Regards, Alexandre Obert -- Alexandre OBERT Doctorant en Psychologie Cognitive Université de Reims Champagne-Ardenne Laboratoire C2S : Cognition, Santé, Socialisation (EA6291) 57, rue Pierre Taittinger - 51096 Reims Cedex - France http://www.univ-reims.fr/C2S

1 0

Any binaries while Martinos disks being repaired / FTP server is down?
by DT 17 Sep '16

17 Sep '16

I tried to download the current freesurfer release from the FTP site, and got a 550 error. After searching, I found the mailing list discussion of the disk problems / server outage with no ETA for its return. (here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046338.html and here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-September/04766… ) Unfortunately, the source code repo, library repo seem unreachable as well. I found an unofficial copy of the source code on github ( https://github.com/neurodebian/freesurfer) but can't compile with the standard ubuntu 14.04 minc library (getting "cannot find miopen: No such file or directory" right now) and my skills at troubleshooting the compilation are... not great. Any chance that - someone can provide the linux distribution file? (i know it's huge) - someone can give me pointers with the library dependencies? - someone knows when the ftp server might be back up? If the packages exist somewhere and the server will be down for a bit, I would be happy to host the FTP site. Please let me know if I can help. Dave

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