Re: [Freesurfer] dt_recon issue

External Email - Use Caution Is this what you mean by no variables?? dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science

Re: [Freesurfer] dt_recon issue

echo "" | & tee -a $LF tee -a echo echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF tee -a echo dt_recon exited with ERRORS at `date` date dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019 echo "" | & tee -a $LF tee -a echo exit

Re: [Freesurfer] dt_recon issue

,Ph.D. < dgr...@mgh.harvard.edu> wrote: > what happens when you run > > ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > On 2/13/19 6:27 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > The e

Re: [Freesurfer] dt_recon issue

, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes. Can you run it with --debug with the slash in front of "Volumes"? > > On 2/13/19 6:25 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > > > Is this what

[Freesurfer] dt_recon error log

scan value [1][1] could not allocate 1684305759 x 1144402954 matrix could not allocate 1684305759 x 1144402954 matrix unsupported matlab format 540094003 (unknown) Any idea what might be causing this error? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain

Re: [Freesurfer] dt_recon error MatrixReadTxT: could not scan value [1][1]

External Email - Use Caution Thanks! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. <

Re: [Freesurfer] anat2dti error after dt_recon

External Email - Use Caution Hi Douglas! Thank you for the response. I figured out it was simply an issue with the pathing to the register.dat file! Thanks, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland

[Freesurfer] Issue posting to the listserve

ubmit from that email so I would like to fix the issue I am having with posting to the listserv with my ddcc2...@gmail.com email address. Thank you, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmai

[Freesurfer] Issue posting to Freesurfer support

ontact to help with this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] Partial Volume Correction for FA map

perform PVC on FA images? Would the --mgx flag need to be changed? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer

Re: [Freesurfer] Partial Volume Correction for FA map

External Email - Use Caution It is a volume based study so I will continue to use mgx .25. Thank you! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Mon

[Freesurfer] dt_recon and mri_vol2vol issue

ges before the registration attempt. Any advice with troubleshooting would be greatly appreciated. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 *Daniel Callow* *P

[Freesurfer] dt_recon --> tbss

peline. My question is are there any steps I should take converting or modifying the FA images so they are compatible with the tbss pipeline. My intention was to take the dt_recon fa or fa-masked into the tbss_1_preproc command? Are there any considerations I should take into account? Best *Dan

[Freesurfer] mask-FA mri_vol2vol issue - followup

diffusion space to anatomical space) would be greatly appreciated. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer

[Freesurfer] MD with dt_recon?

External Email - Use Caution Hello, There is no mean diffusivity output with dt_recon. How would you suggest to create MD images? Could you simply divide the adc.nii.gz map by 3? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health

[Freesurfer] MD with dt_recon

External Email - Use Caution Sorry, I just found in a previous post by doug that ADC is the same as MD? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298

Re: [Freesurfer] MD with dt_recon

External Email - Use Caution Thank you! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Thu, Feb 28, 2019 at 2:56 PM Greve, Douglas N.,Ph.D. <

Re: [Freesurfer] dt_recon --> tbss

e dcm without needing to create the txt files that fsl needed made the preprocessing steps simpler and less likely to lead to human error in the process. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmai

[Freesurfer] dt_recon field map for eddy correct

ing eddy_correct" | tee -a $LF exit 1; endif popd > /dev/null rm -r $ectmp echo "" | tee -a $LF echo "" | tee -a $LF else echo "#@#---" | tee -a $LF echo "Skipping Eddy/Motion Correct" | tee -a $LF

[Freesurfer] citing freesurfer

External Email - Use Caution Hello, How should I go about properly citing freesurfer if I am using dt_recon for dti analysis? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2

[Freesurfer] mri_segstats issue with hippocampal subfields

an provide! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

atlas/compressionLookupTable.txt): badly formed file No such file or directory ERROR: reading /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt any idea how I could make it a formed file that is compatible? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Sc

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Never mind. I see that I can use those to id #'s to call from FreeSurferColorLUT.txt. I assume that those Id's are consistent for both left and right hippocampus. Thanks for the help! *Daniel Callow* *PhD Student, Neuroscience and Cogniti

[Freesurfer] dt_recon multiple dti scans

-- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] recon-all error

provide for troubleshooting would be greatly appreciated. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list

Re: [Freesurfer] recon-all error

External Email - Use Caution Hi Andrew, I am on a mac pro running Sierra 10.12.6 Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Tue, Mar 19, 2019

Re: [Freesurfer] recon-all error

again on the exact same subject Dicoms I may or may not get an error. Any ideas what could be causing this/these errors? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On

[Freesurfer] recon-all could not read surface file error

/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks for any help you can provide with debugging! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2

[Freesurfer] segmentHA_T1_long.sh: Command not found.

. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. *Best,* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254

Re: [Freesurfer] segmentHA_T1_long.sh: Command not found.

External Email - Use Caution Sorry, I realized I did not have the path to freesurfer in my script set to the dev version. It was set to the FS6.0 version. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of

[Freesurfer] segmentHA_T1_long.sh error

If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ A technical support engineer might contact you with further information. Thank you for your help. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for

Re: [Freesurfer] segmentHA_T1_long.sh error {Disarmed}

> > > Research staff > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > > > Research Affiliate > > Computer Science and Artificial Intelligence Laboratory (CSAIL) > > Massachusetts Institute of Technology > > >

[Freesurfer] segmentHA_T1_long.sh HBT issue

.HBT.FSvoxelSpace.mgz and other files for each subject I see only amygdala and subfield segmentations. How do I use the outputs to create a head body and tail segmentation that I can visualize and extract values from?* *Best,* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for

[Freesurfer] segmentHA_T1_long.sh HBT issue

ng at it incorrectly in freeview? Any help is greatly appreciated! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Frees

[Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution The issue was that I was using the freesurfer 6.0 version of freeview and not the development version. Thanks for your help Eugenio! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of

[Freesurfer] segmentHA_T1.sh

? Any help you can provide would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list

[Freesurfer] segmentHA_T1.sh

stats/lhipp_volume.stats Any ideas on how to make this work or a potential other work around. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254

Re: [Freesurfer] segmentHA_T1.sh

External Email - Use Caution Thank you for the suggestion. Is it possible to just calculate certain sub-field volumes such as the head body and tail as opposed to all of them? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab

[Freesurfer] dt_recon ERROR: DTIloadBValues

alues ERROR: DTIloadBValues(dwi.bvals): could not scan value(s) Loading BVectors from dwi.voxel_space.bvecs ERROR: DTIloadBValues(dwi.voxel_space.bvecs): could not scan value(s) Found 0 bvectorss ERROR: DTIloadBValues: no bvectors found in dwi.voxel_space.bvecs Best, *Daniel Callow*

Re: [Freesurfer] dt_recon ERROR: DTIloadBValues

dgr...@mgh.harvard.edu> wrote: > It is having problems reading both the bvals and the bvecs > > On 4/2/19 9:34 AM, Daniel Callow wrote: > > > External Email - Use Caution > > > > Hello, > > > > I am running dt_Recon with the following specifications and am ru

[Freesurfer] Creating anatomical ROI's

d and body segments and extract average diffusion information from the combined mask. Anything that can help get me in the right direction would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College

Re: [Freesurfer] Creating anatomical ROI's

External Email - Use Caution Thank you Doug! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Tue, Apr 9, 2019 at 11:03 AM Greve, Douglas N.,Ph.D. <

[Freesurfer] issue running trac-all longitudinal

Any idea what might be causing the issue? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 # # dmrirc.long.example # # This example is applicable to longitudinal studies, wh

Re: [Freesurfer] issue running trac-all longitudinal

The error does not seem to be due to dwi_orig.nii.gz being missing as I see it in the folderr after it has been written there in a previous command. What could be leading to these issues? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University

Re: [Freesurfer] issue running trac-all longitudinal

External Email - Use Caution Disabling root system integrity protection seems to have solved the problem. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On

Re: [Freesurfer] issue running trac-all longitudinal

tly appreciated. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Fri, Apr 19, 2019 at 8:04 AM Daniel Callow wrote: > Disabling root system integrity protection seems t

[Freesurfer] trac-all running -jobs issue error

2.6.32-696.30.1.el6.x86_64 #1 SMP Fri May 18 11:50:44 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Apr 19 15:45:56 EDT 2019 Any idea why the script might be throwing this error? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exerc

[Freesurfer] epidewarp.fsl error in trac-all script

--vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz portion of the epidewarp.fsl script was not created. Everything else that should go into it was created. Can anyone give me some guidance on why this might be happening? Best, *Daniel Callow* *PhD Student, Neuroscien

[Freesurfer] trac-all -prep b0 inhomogeneity correction error

ths) set FSLToFloatFlag = (-odt float) or are these paramaters different under fsl 6.x+? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 44

[Freesurfer] tractstats2table error

someone please provide me some guidance on how to troubleshoot this? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 /Volumes/DANIEL/trac/Ex.AES101.long.base_AES101

Re: [Freesurfer] tractstats2table error

_table if not 1 == len(pthwyset.keys()): File "/Applications/freesurfer_dev/bin/datastruct_utils.py", line 281, in keys return self.__ksl[:] TypeError: 'dict_keys' object is not subscriptable *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for

[Freesurfer] Citing the development version for use of hippocampal/amygdala sub-field segmentation

cite my use of the development version? And if so how is the best way to go about doing this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail

[Freesurfer] Trac-all error

be causing the issue? Does it seem like tkregister2 isn't working?* *Thank you for help or assistance you can provide.* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254

Re: [Freesurfer] Trac-all error

External Email - Use Caution Hello Anastasia, I was running this on freesurfer's dev version. I will try running it on freesurfer 6.0. Best, *Daniel Callow* *PhD Student, Neuroscience and Conitive Science* Exercise for Brain Health Lab University of Maryland, College Park *

Re: [Freesurfer] Trac-all error

compatibility. Contact the developer for more information. Just FYI. It does work on the freesurfer 6.0 version despite the pop-up. It seems like trac-all is not compatible with the development version then? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain

Re: [Freesurfer] Trac-all error

External Email - Use Caution Thank you for the reply. I guess it is possible that there were some issues with compiling, however I have been using it for a while without issue. I will look into that issue further. Thanks for all your help and feedback! Best, Daniel Callow On Thu

[Freesurfer] TRACULA for kids/children

about this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] TRACULA for kids/children

quick response! Kind regards, Daniel Callow On Mon, Jul 29, 2019 at 6:43 PM Yendiki, Anastasia wrote: > Hi Daniel - What is the age range you're interested in? We have used > tracula with children as young as 5 (see example ref below). Keep in mind > that tracula is not a tradit

[Freesurfer] segmentHA_T2.sh longitudinal version?

HA_T2.sh script to incorporate these types of scans. However, there doesn't seem to be a longitudinal version for this. Is this something that is being worked on? Or is there another reason that T2 should not be used with longitudinal analysis? Thank you for any advice you can provide, *Dan

[Freesurfer] TRACULA incorporate topup instead of field map?

data with topup separately and then incorporate it into TRACULA? Thank you for any guidance you can provide, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.co

Re: [Freesurfer] segmentHA_T2.sh longitudinal version?

External Email - Use Caution Thank you for the prompt answer! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Tue, Jul 30, 2019 at 9:18 AM Iglesias Gonzalez

Re: [Freesurfer] segmentHA_T2.sh longitudinal version?

External Email - Use Caution In that case, would you suggest one to use segmentHA_T1_long.sh instead of segmentHA_T2.sh (cross-sectional) if one has longitudinal data and T2 high-resolution data? Would one be expected to provide superior results? Best, *Daniel Callow* *PhD

Re: [Freesurfer] TRACULA incorporate topup instead of field map?

> -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Tuesday, July 30, 2019 8:44:32 AM > *To:* Freesurfer support list > *Subject:* [Freesurfe

[Freesurfer] segmentHA_T1.sh error

:08:36 EDT 2019 *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] TRACULA - runlist longer than subject list

mage01.dcm HMN189/image01.dcm HMN190/image01.dcm HMN191/image01.dcm HMN193/image01.dcm HMN195/image01.dcm HMN196/image01.dcm HMN200/image01.dcm HMN201/image01.dc) Any help debugging the issue would be greatly appreciated! *Daniel Callow* *PhD Student, Neuros

[Freesurfer] TRACULA - OrientLAS issue for a subject

be? I have looked through this subjects dcminfo.dat file and compared it to others but have been unable to identify the issue. I have also included the trac-all log for this subject. Some advice on what the issue might be would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscienc

Re: [Freesurfer] TRACULA - runlist longer than subject list

Thank you for your help! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Thu, Aug 8, 2019 at 9:07 AM Daniel Callow wrote: > Hello, > > When trying to run TRACUL

[Freesurfer] TRACULA - OrientLAS issue for a subject

doesn't seem to be working for these two subjects. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing

[Freesurfer] TRACULA - OrientLAS issue for a subject

nulify the bvals and bvecs I have and ruin later preprocessing steps? This is the only solution to the problem I have found thus far though. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443

[Freesurfer] TRACULA - input Nifti instead of DICOM?

External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience

Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

they are formatted correctly for TRACULA. Thanks for the reply! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia < ay

[Freesurfer] TRACULA - input Nifti instead of DICOM?

images? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 # # dmrirc.long.example # # This example is applicable to longitudinal studies, where DWI data from # multiple

[Freesurfer] TRACULA error - MRISread could not open file

p. Thank you, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 recon-all-status.log Description: Binary data trac-all.error Description: Binary data trac-all.log Descripti

Re: [Freesurfer] TRACULA error - MRISread could not open file

white file. I just included the recon-all log for that subject to show that recon-all hadn't had any issues. Do you still think it would have to do with recon-all? It seems to have to do with the way Tracula is trying to read the file? Best, *Daniel Callow* *PhD Student, Neuroscience and Co

[Freesurfer] (no subject)

s for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? Best, -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exe

[Freesurfer] b0 to T1’s co-registration without b0 inhommogeneities

s for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? Best, -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exe

[Freesurfer] HBT hippocampal segmentation

subfields. Are there specific anatomical boundary rules that drive the algorithm to differentiate between head and body in the HBT segmentation output. Thank you for any guidance you can provide! Best, *Daniel Callow* *Graduate Student, Neuroscience and Cognitive Science* Exercise for Brain