Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

recon-all | ln -s error
by Pradeep 09 Apr '18

09 Apr '18

Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and recon-all exited with errors at ln -s lh.white.preaparc.H lh.white.H I was not able to perform this operation with sudo as well 4172_vsl/surf$ sudo ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not supported but cp works 4172_vsl/surf$ cp lh.white.preaparc.H lh.white.H has any one come across this problem and what is the best way to fix this? Thanks, Pradeep

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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
by Anna Daniels 09 Apr '18

09 Apr '18

Hi Bruce, hi Srishti, I have exactly the same problem with several subjects rerunning recon-all and there was sufficient memory available. I also tried out the last command directly which resulted in the same error log. mri_normalize -f /home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_ edits_transfer/rreruncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz Attached you can find the input file. Thank you and best, Anna 22275_T1_fs_edit.zip <https://drive.google.com/file/d/1e2KqrnJa56G7Nza9aROpXHM61tjPqnvH/view?usp=…> > can you email us the input file and the full command line you ran? > On Thu, 5 > Apr 2018, srishti goel wrote: > > > So it gave this error: > > > > 3d normalization pass 1 of 2 > > > > white matter peak found at 110 > > > > HISTOalloc(-2147483648): could not allocate histogram > > > > Cannot allocate memory > > > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > > skype: srishti.goel12 > > > > > > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu> wrote: > > let's see if it works. If it does, you should be able to run > > > > recon-all -s SUBJID -make all > > > > cheers > > Bruce > > > > > > On Thu, 5 Apr 2018, srishti goel wrote: > > > > Should I re-run the recon-all after running the last command > from recon-all.cmd? > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu > > skype: srishti.goel12 > > > > > > On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu> wrote: > > ? ? ? Hi Srishti > > > > ? ? ? if you look in the subject's scripts dir there should > be a file named "recon-all.cmd". Try > > rerunning the last > > ? ? ? command in it (probably from the mri dir) > > > > ? ? ? cheers > > ? ? ? Bruce > > ? ? ? On Thu, 5 Apr 2018, srishti goel wrote: > > > > ? ? ? ? ? ? I am sorry, I am not sure what do you mean by > running the command line directly? > > ? ? ? ? ? ? I use the following command: > > > > ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END > --mail-user srishtig(a)email.unc.edu --wrap > > "export > > ? ? ? ? ? ? SUBJECTS_DIR=/proj/hng/sherida > nlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166 > > ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa" > > > > > > ? ? ? ? ? ? where sbatch..... until export is our local > server submission command and I run this > > command from the > > ? ? ? ? ? ? command line itself, not > > ? ? ? ? ? ? using any script. > > > > > > ? ? ? ? ? ? Best, > > ? ? ? ? ? ? Srishti > > ? ? ? ? ? ? Social/Clinical Research Specialist > > ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab > > ? ? ? ? ? ? University of North Carolina at Chapel Hill > > ? ? ? ? ? ? email (W): srishtig(a)email.unc.edu > > ? ? ? ? ? ? skype: srishti.goel12 > > > > > > ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu> wrote: > > ? ? ? ? ? ? ? ? ? if you run the command that failed again > on the command line directly (that is, not > > in > > ? ? ? ? ? ? recon-all) does it fail > > ? ? ? ? ? ? ? ? ? again? > > > > ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote: > > > > ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce, > > > > ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run > out of memory. Here is the memory usage > > ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ? > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? > ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ? > > ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available > > ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ? > 152102696 ? ? ? 12944 ? ?77294224 ? > > ? ? ? ? ? ? ? ? ? ? ? ? 191963372 > > ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? > ? ? ? ? 2097148 > > > > > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? Best, > > ? ? ? ? ? ? ? ? ? ? ? ? Srishti > > ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist > > ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life > Experiences Lab > > ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at > Chapel Hill > > ? ? ? ? ? ? ? ? ? ? ? ? email (W): srishtig(a)email.unc.edu > > ? ? ? ? ? ? ? ? ? ? ? ? skype: srishti.goel12 > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:16 PM, > Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > ? ? ? ? ? ? ? ? ? ? ? ? wrote: > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Srishti > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? are you sure that your machine > didn't just run out of memory? > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? The recon-all.log file > includes the amount of free (and total) > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? memory at the time the process > was started. > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cheers > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Bruce > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?On Thu, 5 Apr 2018, srishti > goel wrote: > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi, > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I have been trying to > edit structural brains and > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? very few times I would > get the following error while > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? running recon-all -s > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? subjID > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? white matter peak found > at 110 > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cannot allocate memory > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Upon looking at the > archive, there was only one > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? similar issue and it was > recommend to check mri_info > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? as the brain mask might > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? have been corrupted. I > did that and here is the > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? output: > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Volume information for > brainmask.mgz > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: MGH > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? dimensions: 256 x > 256 x 256 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? voxel sizes: > 1.000000, 1.000000, 1.000000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: UCHAR (0) > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? dof: 0 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xstart: -128.0, > xend: 128.0 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ystart: -128.0, > yend: 128.0 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? zstart: -128.0, > zend: 128.0 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 > msec, TE: 0.00 msec, TI: 0.00 > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? msec, flip angle: 0.00 > degrees > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? nframes: 1 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? FieldStrength: > 0.000000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras xform present > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xform info: x_r =? > -1.0000, y_r = ? 0.0000, z_r > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_r =? ? > -1.0000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? > 0.0000, y_a = ? 0.0000, z_a > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 1.0000, c_a =? ? > 37.5000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? > 0.0000, y_s =? -1.0000, z_s > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_s = ? ? > 4.7185 > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? talairach xfm > > ? ? ? ? ? ? :/pine/scr/s/r/srishtig/Duke_T > est/Freesurfer_out/11039/mri/transforms/talair > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ach.xfm > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Orientation ? : LIA > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Primary Slice Direction: > coronal > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel to ras transform: > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 ? > 0.0000 ? 0.0000 ? 127.0000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? > 0.0000 ? 1.0000 ? -90.5000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? > -1.0000 ? 0.0000 ? 132.7185 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? > 0.0000 ? 0.0000 ? ? 1.0000 > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel-to-ras determinant > -1 > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras to voxel transform: > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? > -0.0000? -0.0000 ? 127.0000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? > -0.0000? -1.0000 ? 132.7185 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 ? > 1.0000? -0.0000? ? 90.5000 > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? > -0.0000? -0.0000 ? ? 1.0000 > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Is there any other way > to resolve this issue than > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? reconstruction the brain > again and doing all the > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? edits all over again > hoping > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? that the?brain mask does > not get corrupted this > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? time? > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Appreciate any help with > this. > > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Best, > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Srishti > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? ______________________________ > _________________ > > ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer mailing list > > ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer(a)nmr.mgh.harvard.edu > > ? ? ? ? ? ? ? ? ? ? ? ? https://mail.nmr.mgh.harvard.e > du/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/compli > anceline . If the e-mail was sent to you > > ? ? ? ? ? ? ? ? ? ? ? ? in error > > ? ? ? ? ? ? ? ? ? ? ? ? but does not contain patient > information, please contact the sender > > ? ? ? ? ? ? ? ? ? ? ? ? and properly > > ? ? ? ? ? ? ? ? ? ? ? ? dispose of the e-mail. > > > > > > > > > > ? ? ? ? ? ? _______________________________________________ > > ? ? ? ? ? ? Freesurfer mailing list > > ? ? ? ? ? ? Freesurfer(a)nmr.mgh.harvard.edu > > ? ? ? ? ? ? https://mail.nmr.mgh.harvard.e > du/mailman/listinfo/freesurfer > > > > > > ? ? ? ? ? ? The information in this e-mail is intended only > for the person to whom it is > > ? ? ? ? ? ? addressed. If you believe this e-mail was sent > to you in error and the e-mail > > ? ? ? ? ? ? contains patient information, please contact the > Partners Compliance HelpLine at > > ? ? ? ? ? ? http://www.partners.org/complianceline . If the > e-mail was sent to you in error > > ? ? ? ? ? ? but does not contain patient information, please > contact the sender and properly > > ? ? ? ? ? ? dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to whom it is > > addressed. If you believe this e-mail was sent to you in > error and the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > > but does not contain patient information, please contact the > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > ------------------------------ > >

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mri_glmfi-sim multi-thread
by Dowling, Kevin Francis 08 Apr '18

08 Apr '18

Dear Freesurfer Experts, My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)? We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05) Thank you in advance for your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215

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Three Postdoctoral or PhD positions in Stochastic Signal Processing/Computational Modelling fMRI/EEG
by Shankar Tumati 06 Apr '18

06 Apr '18

Three postdoctoral (or graduate) positions are available at the Mind, Brain Imaging & Neuroethics lab. The candidates should have strong background in brain imaging (fMRI, MRS, EEG/MEG, TMS) and preferably strong education in neuroscience/brain imaging, engineering, physics, and/or computational neuroscience for data analyses. The project focuses on resting state and its interaction with task-evoked activity in relation to mental features like self and consciousness in both healthy and psychiatric subjects where neuronal, electrophysiological and biochemical measures will be obtained. A specific focus will be on novel ways of dynamic and non-linear analyses of the brain imaging data in conjunction with computational modeling and signal processing analyses. Part of the project will be carried out in China at Zhejiang University in Hangzhou/China and, in part, in Ottawa/Canada as the PI has affiliations with both places. Hence, Chinese skills are of advantage but not a prerequisite for application. More information about our work can be found on the website: www.georgnorthoff.com For PhD candidates. Graduation at University of Ottawa (PhD) under the supervision of Dr. G. Northoff is possible. Salary for the postdoctoral candidates depends on qualifications and will be around 35.000 CAD to 70.000 CAD. Outstanding candidates may also qualify for faculty position in China. Candidates shall contact: Dr. G. Northoff: georg.northoff(a)theroyal.ca (website: www.georgnorthoff.com)

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Time Series to Surface
by Crawford, Anna 06 Apr '18

06 Apr '18

Hello, I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume? Thanks for your help, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). 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.

3 10

FSGD design for multi-centre study
by C.P.E. Rollins 06 Apr '18

06 Apr '18

Dear Freesurfer Developers, I'd like to do a standard CT analysis (patients vs. controls, covaried for age and sex) on data from a multi-centre study and I'm wondering how I should construct my FSGD file to code centre as a dummy variable. Currently, my FSGD looks something like this: GroupDescriptorFile 1 Group Control_Male Group Control_Female Group Patient_Male Group Patient_Female Variables Age Input subj001-002 Patient_Male 32 Input subj001-003 Patient_Male 19 Input subj001-040 Patient_Female 28 ... To include centre as dummy variable, would I add an additional column for each centre and enter either a 1 or a 0 depending on whether that scan is from that centre? For instance, there were 6 centres (scans for patients and controls collected at each) in the study, so centre as a dummy variable might look something like this (columns added on after age)? 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 Moreover, would this be the best way to control for centre? Many thanks, Colleen

2 1

Quality of fMRI registration
by Arsenije Subotic 06 Apr '18

06 Apr '18

Dear experts, When it comes to assessing the quality of fMRI integration in Freesurfer, is a value of > 0.5 considered a good registration? I was led to believe that from the multimodal tutorial website, and after checking the quality of my output I was satisfied with the result for each of my participants. However, I came back to the multimodal tutorial later after two weeks, and noticed that the page had been edited and now it says that any value <0.5 is considered a good registration. How would I go about resolving this issue, seeing as I visually inspected my output after each automatic registration and everything seemed fine? Most of my registration values were about 0.5-0.6. Please let me know. Thanks! Arsenije

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Tracula - Could not find satisfactory control point fit
by Lussier,Desiree 06 Apr '18

06 Apr '18

Dear Freesurfer experts, I have been trying run trac-all -prep on two subjects but it seems to be stuck on the priors pathway estimation. The following (with updated number of tries) keeps appearing in the terminal: WARN: Could not find satisfactory control point fit - try 288 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels I've attached the log here. Previous communications I've seen regarding this are years old and were solved by upgrading to 5.3. However, I'm already using the 64 bit 6.0. Advice regarding this situation would be greatly appreciated. Thank you, Desiree Lussier

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Re: [Freesurfer] scan log generated by dcmunpack
by Kan Ding 05 Apr '18

05 Apr '18

The data has been analyzed. The scan information from corresponding NIFTI file as following: nua502608:3T8619 kding$ mri_info 3T8619_T1.nii.gz Volume information for 3T8619_T1.nii.gz type: nii dimensions: 160 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 160.000 dof: 0 xstart: -80.0, xend: 80.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = 0.0107 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 7.8592 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -15.4014 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 -0.0000 -0.0000 80.0107 -0.0000 -1.0000 -0.0000 135.8592 0.0000 0.0000 1.0000 -143.4014 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 80.0107 0.0000 -1.0000 0.0000 135.8592 0.0000 0.0000 1.0000 143.4014 0.0000 0.0000 0.0000 1.0000 Date: Thu, 5 Apr 2018 12:59:16 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] scan log generated by dcmunpack To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <22ecfa88-e463-169b-03c5-4c25ac2244db(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252"; format=flowed It looks like there is something wrong with that dicom file/series because the pixel spacing is "unknown". Where did the dicoms from from? Have they been anonymized? On 04/05/2018 12:12 PM, Kan Ding wrote: >Hello: > >I am trying to unpack my DICOM folder and run recon-all. After >dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t >go through. Please see the attached scan.log, recon-all.log, >error.log, and the pic of my DICOM folder. > >Thank you so mch. > >Kan Ding, MD > On 4/5/18, 3:21 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <reesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: >Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > >To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/istinfo/freesurfer >or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > >You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. scan log generated by dcmunpack (Kan Ding) > 2. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (Bruce Fischl) > 3. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (srishti goel) > 4. Qdec+Table format issue ????? (Dimitrios Trifonopoulos) > 5. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (Bruce Fischl) > 6. Re: recon-all: exited with errors (whit matter peak at 110, > cannot allocate memory) (srishti goel) > 7. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (Bruce Fischl) > 8. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (srishti goel) > 9. Re: recon-all: exited with errors (white matterpeak at 110, > cannot allocate memory) (Bruce Fischl) > 10. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (srishti goel) > 11. Re: recon-all: exited with errors (white matter peak at 110, > cannot allocate memory) (Bruce Fischl) > 12. Re: mri_vol2surf: unable to compare volume maps (Douglas N. Greve) > 13. Re: scan log generated by dcmunpack (Douglas N. Greve) > 14. Time Series to Surface (Crawford, Anna) > 15. Tracula - Could not find satisfactory control point fit > (Lussier,Desiree) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 5 Ap 2018 16:12:43 +0000 >From: Kan Ding <Kan.Ding(a)utsouthwestern.edu> >Subject: [Freesurfer] scan log generated by dcmunpack >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <D6EBC339.10FF3%kan.ding(a)utsouthwestern.edu> >Contnt-Type: text/plain; charset="iso-8859-1" > >Hello: > >I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, >I selected 301 to run recon-all. But the recon-all didn't go through. >Please see the attached scan.log, recon-all.log, error.log, and the pic >of my DICOM folder. > >Thank you so much. >Kan Din, MD >Assistant Professor- Department of Neurology and Neurotherapeutics >UT Southwestern Medical Center at Dallas >Tel: 214-648-9197 >Fax: 214-648-6320 > >________________________________ > >UT Southwestern > > >Medical Center > > > >The future of medicine, today. > >

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scan log generated by dcmunpack
by Kan Ding 05 Apr '18

05 Apr '18

Hello: I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, I selected 301 to run recon-all. But the recon-all didn't go through. Please see the attached scan.log, recon-all.log, error.log, and the pic of my DICOM folder. Thank you so much. Kan Ding, MD Assistant Professor- Department of Neurology and Neurotherapeutics UT Southwestern Medical Center at Dallas Tel: 214-648-9197 Fax: 214-648-6320 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Freesurfer