Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

Using only a aparc+aseg input file for TRACULA
by Alexopoulos, Dimitrios 21 Oct '21

21 Oct '21

External Email - Use Caution Hi, It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. Is this correct? How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs? For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file). Jim ________________________________ 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.

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Dracula 7.2 -bedp error
by Chong, Catherine (Cat), Ph.D. 21 Oct '21

21 Oct '21

External Email - Use Caution Dear Tracula team, I am running 7.2 on a computing cluster and the -prep stage completes without error. The dmri directory show the following files, below. However, after running the second step ( -bedp), the files under dmri.bedpostX do not appear to have merged. (bvals bvecs cancel commands.txt diff_slices logs monitor xfms). I am not able to find any error messages and the bedpostx_post.o529573 log is below. I have also attached my script to the very bottom. I would be grateful for your guidance in helping me solve this problem. Cat Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value -n <N> : only use volume <N> from each input file (first volume is 0 not 1) Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value -n <N> : only use volume <N> from each input file (first volume is 0 not 1) Removing intermediate files Creating identity xfm Done ~ brain_anat_mni.nii.gz data_slice_0018.nii.gz data_slice_0042.nii.gz dcminfo.dat lowb_brain.nii.gz nodif_brain_mask_slice_0021.nii.gz nodif_brain_mask_slice_0045.nii.gz brain_anat.nii.gz data_slice_0019.nii.gz data_slice_0043.nii.gz dtifit_FA.nii.gz lowb.nii.gz nodif_brain_mask_slice_0022.nii.gz nodif_brain_mask_slice_0046.nii.gz brain_anat_orig.nii.gz data_slice_0020.nii.gz data_slice_0044.nii.gz dtifit_L1.nii.gz nodif_brain_mask.nii.gz nodif_brain_mask_slice_0023.nii.gz nodif_brain_mask_slice_0047.nii.gz bvals data_slice_0021.nii.gz data_slice_0045.nii.gz dtifit_L2.nii.gz nodif_brain_mask_slice_0000.nii.gz nodif_brain_mask_slice_0024.nii.gz nodif_brain_mask_slice_0048.nii.gz bvecs data_slice_0022.nii.gz data_slice_0046.nii.gz dtifit_L3.nii.gz nodif_brain_mask_slice_0001.nii.gz nodif_brain_mask_slice_0025.nii.gz nodif_brain_mask_slice_0049.nii.gz data.nii.gz data_slice_0023.nii.gz data_slice_0047.nii.gz dtifit_MD.nii.gz nodif_brain_mask_slice_0002.nii.gz nodif_brain_mask_slice_0026.nii.gz nodif_brain_mask_slice_0050.nii.gz data_slice_0000.nii.gz data_slice_0024.nii.gz data_slice_0048.nii.gz dtifit_MO.nii.gz nodif_brain_mask_slice_0003.nii.gz nodif_brain_mask_slice_0027.nii.gz nodif_brain_mask_slice_0051.nii.gz data_slice_0001.nii.gz data_slice_0025.nii.gz data_slice_0049.nii.gz dtifit_S0.nii.gz nodif_brain_mask_slice_0004.nii.gz nodif_brain_mask_slice_0028.nii.gz nodif_brain_mask_slice_0052.nii.gz data_slice_0002.nii.gz data_slice_0026.nii.gz data_slice_0050.nii.gz dtifit_V1.nii.gz nodif_brain_mask_slice_0005.nii.gz nodif_brain_mask_slice_0029.nii.gz nodif_brain_mask_slice_0053.nii.gz data_slice_0003.nii.gz data_slice_0027.nii.gz data_slice_0051.nii.gz dtifit_V2.nii.gz nodif_brain_mask_slice_0006.nii.gz nodif_brain_mask_slice_0030.nii.gz nodif_brain_mask_slice_0054.nii.gz data_slice_0004.nii.gz data_slice_0028.nii.gz data_slice_0052.nii.gz dtifit_V3.nii.gz nodif_brain_mask_slice_0007.nii.gz nodif_brain_mask_slice_0031.nii.gz nodif_brain_mask_slice_0055.nii.gz data_slice_0005.nii.gz data_slice_0029.nii.gz data_slice_0053.nii.gz dwi.bvals nodif_brain_mask_slice_0008.nii.gz nodif_brain_mask_slice_0032.nii.gz nodif_brain_mask_slice_0056.nii.gz data_slice_0006.nii.gz data_slice_0030.nii.gz data_slice_0054.nii.gz dwi.bvecs nodif_brain_mask_slice_0009.nii.gz nodif_brain_mask_slice_0033.nii.gz nodif_brain_mask_slice_0057.nii.gz data_slice_0007.nii.gz data_slice_0031.nii.gz data_slice_0055.nii.gz dwi.ecclog nodif_brain_mask_slice_0010.nii.gz nodif_brain_mask_slice_0034.nii.gz nodif_brain_mask_slice_0058.nii.gz data_slice_0008.nii.gz data_slice_0032.nii.gz data_slice_0056.nii.gz dwi_motion_byvol.txt nodif_brain_mask_slice_0011.nii.gz nodif_brain_mask_slice_0035.nii.gz nodif_brain_mask_slice_0059.nii.gz data_slice_0009.nii.gz data_slice_0033.nii.gz data_slice_0057.nii.gz dwi_motion.txt nodif_brain_mask_slice_0012.nii.gz nodif_brain_mask_slice_0036.nii.gz nodif_brain_mask_slice_0060.nii.gz data_slice_0010.nii.gz data_slice_0034.nii.gz data_slice_0058.nii.gz dwi.nii.gz nodif_brain_mask_slice_0013.nii.gz nodif_brain_mask_slice_0037.nii.gz nodif_brain_mask_slice_0061.nii.gz data_slice_0011.nii.gz data_slice_0035.nii.gz data_slice_0059.nii.gz dwi_orig.1.bvals nodif_brain_mask_slice_0014.nii.gz nodif_brain_mask_slice_0038.nii.gz nodif_brain_mask_slice_0062.nii.gz data_slice_0012.nii.gz data_slice_0036.nii.gz data_slice_0060.nii.gz dwi_orig.1.bvecs nodif_brain_mask_slice_0015.nii.gz nodif_brain_mask_slice_0039.nii.gz nodif_brain_mask_slice_0063.nii.gz data_slice_0013.nii.gz data_slice_0037.nii.gz data_slice_0061.nii.gz dwi_orig.1.nii.gz nodif_brain_mask_slice_0016.nii.gz nodif_brain_mask_slice_0040.nii.gz nodif_brain_mask_slice_0064.nii.gz data_slice_0014.nii.gz data_slice_0038.nii.gz data_slice_0062.nii.gz dwi_orig_las.bvals nodif_brain_mask_slice_0017.nii.gz nodif_brain_mask_slice_0041.nii.gz nodif_brain_mask_slice_0065.nii.gz data_slice_0015.nii.gz data_slice_0039.nii.gz data_slice_0063.nii.gz dwi_orig_las.bvecs nodif_brain_mask_slice_0018.nii.gz nodif_brain_mask_slice_0042.nii.gz xfms data_slice_0016.nii.gz data_slice_0040.nii.gz data_slice_0064.nii.gz dwi_orig_las.nii.gz nodif_brain_mask_slice_0019.nii.gz nodif_brain_mask_slice_0043.nii.gz data_slice_0017.nii.gz data_slice_0041.nii.gz data_slice_0065.nii.gz dwi_snr.txt nodif_brain_mask_slice_0020.nii.gz nodif_brain_mask_slice_0044.nii.gz ! /bin/bash #$ -N recon-all #$ -cwd #$ -o /research/ freesurfer/logs_$TASK_ID #$ -e /research/ /freesurfer/logs_$TASK_ID #$ -j y #$ -M xx(a)mayo.edu #$ -m abe ###$ -pe threaded 4 #$ -notify #$ -l h_vmem=20G #$ -V #$ -l h_stack=20M #$ -t 1 set -x curr_subj=$(sed -n "${SGE_TASK_ID}p" /research/labs/neurology/cat/freesurfer/subjects/subject_list3) echo $curr_subj export FREESURFER_HOME=/usr/local/biotools/freesurfer/freesurfer-v7.2.0 export SUBJECTS_DIR=/research/labs/neurology/cat/freesurfer/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh export FSLDIR="/usr/local/biotools/fsl/6.0.5/" source ${FSLDIR}/etc/fslconf/fsl.sh export PATH="${FSLDIR}/bin:${FREESURFER_HOME}/bin:$PATH" export FSLDIR PATH unset PROFILE cat > config << END set dtroot = $SUBJECTS_DIR/Tracula set subjlist = DODHC09_1_out set dcmroot = $SUBJECTS_DIR/$curr_subj set dob0 = 0 set doeddy = 1 set interreg = 1 END trac-all -path -i $SUBJECTS_DIR/$curr_subj/IM-0003-0001.dcm -subject ${curr_subj} -c config

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Re: [Freesurfer] developer password of Freesurfer VBOx
by fsbuild 20 Oct '21

20 Oct '21

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 11:11, byu <byu(a)cmu.edu.cn> wrote:        External Email - Use Caution        I am radiologist of Shengjing hospital of China Medical University. I am now  attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account. Would you be able to provide a password please?Thanks！Bing Yubyubyu@cmu.edu.cn签名由网易邮箱大师定制_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] developer password
by fsbuild 20 Oct '21

20 Oct '21

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 10:31, Joshua Ericson <josheric(a)hssdschools.org> wrote:        External Email - Use Caution        I am attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account, while installation guide assumes automatic login. Would you be able to provide a password please?Joshua Ericson Technology EducationBay Port High School_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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remove my email from mailing list
by Salah Showiheen 20 Oct '21

20 Oct '21

External Email - Use Caution Thank you

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Re: [Freesurfer] developer password of Freesurfer VBOx
by fsbuild 20 Oct '21

20 Oct '21

External Email - Use Caution Sending the info to your private emails shortly. -R. On Oct 20, 2021, at 11:20, Joshua Ericson <josheric(a)hssdschools.org> wrote:        External Email - Use Caution        I am having the same issue.  Please, provide the password to me as well.Thank you,Joshua Ericson Technology EducationBay Port High SchoolOn Wed, Oct 20, 2021 at 10:12 AM byu <byu(a)cmu.edu.cn> wrote:        External Email - Use Caution        I am radiologist of Shengjing hospital of China Medical University. I am now  attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account. Would you be able to provide a password please?Thanks！Bing Yubyubyu@cmu.edu.cn签名由网易邮箱大师定制_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JuXEI1J3m_Xz-068z2AU_Bt67Ix5Bu7mRls-q… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Specialist in Affective Neuroscience
by CHM Recruiting 20 Oct '21

20 Oct '21

External Email - Use Caution Research Specialist in Affective Neuroscience Are you interested in how emotional and brain processes are related to life experiences, cognition, health, and well-being? The Research Specialist will be responsible for scientific integrity of data collection, data cleaning, and data processing for the Emotion and Wellness Study, led by Dr. Stacey Schaefer, at the University of Wisconsin-Madison's Center for Healthy Minds. Data collection includes in-person study visits, working with a participant one-on-one collecting a variety of questionnaires, cognitive/behavioral tasks, biomarkers (e.g. saliva and dried blood spots), psychophysiology (e.g. facial electromyography, heartrate, respiration and skin conductance), and neuroimaging (e.g. functional and structural MRI). This position requires good people and communication skills, and flexibility to work with people from a wide age-range and different backgrounds. Opportunities exist to learn a variety of data processing techniques and skills. Please go to https://secure-web.cisco.com/19GlcpQW-8522vXVxtPKYbaN1P-EXz3_3pQvGw_9BNnirk… to view the complete job posting and apply online. Deadline to apply is November 2, 2021. UW-Madison is an affirmative action/equal employment employer and we encourage women, minorities, veterans, and people with disabilities to apply.

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Re: [Freesurfer] developer password of Freesurfer VBOx
by Joshua Ericson 20 Oct '21

20 Oct '21

External Email - Use Caution I am having the same issue. Please, provide the password to me as well. Thank you, Joshua Ericson Technology Education Bay Port High School On Wed, Oct 20, 2021 at 10:12 AM byu <byu(a)cmu.edu.cn> wrote: > External Email - Use Caution > > I am radiologist of Shengjing hospital of China Medical University. I am > now attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, > but it requests a login password for the "Developer" account. Would you be > able to provide a password please? > > Thanks！ > Bing Yu > > > byu > byu(a)cmu.edu.cn > > <https://secure-web.cisco.com/14OJp-a8fj-GVHMPXYNjRTEM-GL9ypoh0kiK-79kbg11vY…> > 签名由网易邮箱大师 > <https://secure-web.cisco.com/1Q8cBIeqUS9qaZOi-WF3hVqQx3pLZPX4E3GDLXTN7gGBUr…> > 定制 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1kMRKJUzI8ewAZEMQxp0stB4DyjXKf0jGseRwdg-vgB8o_…

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developer password of Freesurfer VBOx
by byu 20 Oct '21

20 Oct '21

1 0

developer password
by Joshua Ericson 20 Oct '21

20 Oct '21

External Email - Use Caution I am attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account, while installation guide assumes automatic login. Would you be able to provide a password please? Joshua Ericson Technology Education Bay Port High School

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Freesurfer October 2021